Convention: Since I will be asking about some technicalities around Turing machines, it behooves to give a precise definition: say, here, “Turing machine” will stand for a $2$-symbol $1$-tape machine with $m$ states for some $m\geq 1$, its program is a function $\delta \colon Q \times \Sigma \to (Q\cup \{0\}) \times \Sigma \times \{ \mathtt{L}, \mathtt{R} \}$ where $Q = \{1,\ldots,m\}$ is the set of states, $\Sigma = \{0,1\}$ is the set of tape symbols and $\mathtt{L}, \mathtt{R}$ stand for the directions left and right in which the head may move. The tape will always be filled with $0$'s except for finitely many $1$'s. The machine always starts execution in state $1$ and stops when it reaches the state $0$.
We know Turing machines can compute any computable function, in the sense that there is a proper encoding of input and output values such that any computable function can be computed by some program. Very specifically, for each $f \colon \mathbb{N} \dashrightarrow \mathbb{N}$ partial computable, there is a Turing machine $M_f$ such that if $M_f$ is run from a tape containing the number $x$ written in unary immediately after the starting head position (i.e., the tape starts as $1^x$ with the head at the leftmost $1$, and the rest is filled with $0$'s), the machine terminates in finite time iff $f(x) =: y$ is defined, and, if so, returns a tape in the form $1^y$ with the head at the same position as initially.
When studying computability, the details of the encoding aren't very interesting, but the point is some encoding is necessary and it can't be arbitrary:
Definition: Let us say that two computable injections $\gamma_{\mathrm{i}}$ and $\gamma_{\mathrm{o}}$ (the “input encoding” and “output encoding” respectively) of $\mathbb{N}$ in the set of all possible tapes with only finitely many $1$'s on them (together with a marked head position) are a (computably) proper encoding [my terminology] when, for any $f \colon \mathbb{N} \dashrightarrow \mathbb{N}$ partial computable, there is a Turing machine $M_f$ such that $M_f$ terminates on $\gamma_{\mathrm{i}}(x)$ iff $f(x) =: y$ is defined and in this case leaves the tape as $\gamma_{\mathrm{o}}(y)$. [See remarks at end for the definition of what it means for $\gamma_{\mathrm{i}}$ and $\gamma_{\mathrm{o}}$ to be “computable”.]
So the unary encoding ($x \mapsto 1^x$) for input and output is proper. But it is emphatically not true that for any computable injections $\gamma_{\mathrm{i}}$ and $\gamma_{\mathrm{o}}$ define a proper encoding. For example, here's something you can't do with a Turing machine because the input encoding is wrong: if the integer $n \geq 1$ is encoded as a single $1$ at $n$ positions to the right of the starting head position whereas the number $0$ is encoded as a completely blank tape (i.e., $\gamma_{\mathrm{i}}(n) = 0^n 1$ for $n\geq 1$ and $\gamma_{\mathrm{i}}(0) = 0$), then the function $\mathbf{1}_{\{0\}} \colon \mathbb{N} \to \mathbb{N}$ (with value $1$ at $0$ and $0$ elsewhere) cannot be computed by a Turing machine with this (silly) encoding because the machine can never be sure if there is a $1$ somewhere on the tape: so distinguishing a nonzero value becomes semi-computable and no longer computable for (input) encoding reasons.
I suspect there are also limitations due to the output encoding. Specifically, I suspect that if $\gamma_{\mathrm{o}}$ is surjective (any tape configuration is attained). it can never be part of a proper encoding. (The reason for my belief is that the Turing machine needs to use its tape as memory even as part of the writing process, so if you ask it to be able to write any tape, something will conflict with the use as memory. But I have not been able to make this argument precise.)
Anyway, my QUESTIONS are:
Is there a standard term for what I call “computably proper” encodings above? Has the notion been studied in any detail?
Is it correct that there are limitations due to the output encoding and not just the input one? Namely, that not every $\gamma_{\mathrm{o}}$ can be part of a proper encoding? Specifically, is it correct that a surjective $\gamma_{\mathrm{o}}$ is never proper (or at least isn't when $\gamma_{\mathrm{i}}$ is the unary encoding)?
Even the following point escapes me: is the condition “$(\gamma_{\mathrm{i}}, \gamma_{\mathrm{o}})$ is proper” the conjunction of a property on $\gamma_{\mathrm{i}}$ and one on $\gamma_{\mathrm{o}}$?
Remarks (2023-11-19): The question has now been satisfactorily answered, but let me clarify a few points that have been raised in the comments.
✱ “What does it mean for $\gamma_{\mathrm{i}}$ and $\gamma_{\mathrm{o}}$ to be computable?”
I didn't want to lengthen the question by defining a notion that I think is standard, but since the context led to a lot of misunderstanding, here it is:
A map $\gamma$ from $\mathbb{N}$ to the set $\mathrm{Tape}$ of all possible tapes with only finitely many $1$'s on them (together with a marked head position) is computable when $\gamma = \gamma_{\mathrm{std}} \circ g$ where $g \colon \mathbb{N} \to \mathbb{N}^2$ is a computable function (in the standard sense, e.g., Herbrand-Gödel-Kleene general recursive) and $\gamma_{\mathrm{std}} \colon \mathbb{N}^2 \to \mathrm{Tape}$ takes a pair of natural numbers $n_0,n_1$ and returns the tape where $n_0$ is written in binary, left-to-right with the least significant bit first, starting from the head position, and $n_1$ is written in binary, right-to-left with the least significant bit first, starting just left of the head position (so for example $\gamma_{\mathrm{std}}(26,14)$ produces the tape $1110\underline{0}1011$ with the head at the underlined $0$, since $26$ is $11010$ in binary and $14$ is $1110$ in binary, all other symbols being, of course, $0$).
Sorry for the excruciating details here, which of course aren't important (this is what anyone would call a “computable” function from $\mathbb{N}$ to $\mathrm{Tape}$), but the context of the question seems to have caused confusion. The important thing is that from $n$ we can compute any reasonable complete description of $\gamma(n)$ and $\gamma_{\mathrm{std}}$ is just there to formalize what I mean by a “reasonable complete description” without waving my hands: we need to be able to compute the list of all $1$'s on the tape (relative to the head position).
Note that $\gamma_{\mathrm{std}}$ is not proper as an input encoding (this is probably what caused much of the confusion): indeed, I need it to be surjective to define all other computable encodings, and if $\gamma_{\mathrm{std}}$ were proper then any encoding would be proper, which is ont the case as I point out.
✱ “What is the point of this question?”
Of course this doesn't tell us anything new about computable functions but it tells us something about what Turing Machines can do. Turing machines can compute exactly computable functions when (and only when) we use a proper encoding, but if we're interested in Turing Machines per se (and not just as an instrument to define computable functions) and what they can do, then I think it's at least worth taking the time to ask what it means for an encoding to be “proper” rather than imposing it once and for all (as in the unary encoding).
Given the historical importance of Turing Machines, I think it's worth trying to understand a bit more precisely how input and output encodings affect what they can do.
Specifically, this question occurred in my teaching in at least two contexts:
Clearing up confusion on the students' part regarding the issue “how come a Turing machine can't detect whether there's the tape is entirely blank whereas any singleton is decidable?” — I think this is a very valid issue to be raised (at least when teaching) and this concerns the input encoding.
Trying to write an exercise of the form “show that there is a Turing machine which writes its own program on the tape, then stops”, where I wanted the output format to be something a little more transparent than a number in unary that encodes the program in a complicated way (which pedagogically seems very much like cheating): but for the exercise to work we need to chose an output encoding that is proper (and thanks to Joel David Hamkins's answer, we know that any one will do).