This answer expands on Chandra's comment. We'll prove two lemmas that show that $q=O(\log m)$ is a necessary condition for Properties (1) and (2) to hold, and that this bound is tight in the sense that there are infinitely many instances $X$ having Properties (1) and (2) with $q=\Theta(\log m)$. The proofs use known Set-Cover LP integrality gaps, per Chandra's comment.
Lemma 1. If Properties (1) and (2) hold, then $q = O(\log m)$.
Lemma 2. There are infinitely many instances $X$ such that (1) and (2) hold and $q= \Omega(\log m)$.
For the proofs, fix any $(m, n, q, \alpha)$ and "instance" $X$ as in the post. Let LP denote the standard linear-program relaxation of the standard integer linear program for the Set Cover instance defined by the set system $X$ (in which each element must be covered at least once).
Proof of Lemma 1. Let $\overline X$ be the (fractional) LP solution that gives weight $1/q$ to each set in $X$. By Property (1), $\overline X$ is feasible for the LP. It is well-known that the integrality gap of the LP is at most $H_m$. (This is provable by, e.g., randomized rounding or the standard greedy algorithm.) So there is a set cover of size at most $H_m$ times the size of $\overline X$, that is, at most $H_m |X|/ q = H_m n/ q$.
By Property (2), then, $H_m n/q > \alpha n$. That is, $q < H_m / \alpha$. Since $\alpha$ is a positive constant, $q= O(\log m)$. $~~~\Box$
Proof of Lemma 2. Now fix any particular Set-Cover instance for which the integrality gap of the LP is achieved (that is, any set cover for the instance has size at least $H_m$ times the value of the LP for the instance). (It is well known that there are infinitely many such instances.)
Let $\overline X$ be an optimal fractional solution for the LP for this instance.
By definition of the integrality gap,
any set cover for the instance has size at least $\overline n = \lceil |\overline X|H_m\rceil$,
where $|\overline X|=\sum_s \overline X_s$ is the value of $\overline X$.
Let $X$ be the random multiset obtained by taking,
say, $n = 100\overline n$ sets i.i.d.
from the distribution $\overline X / |\overline X|$.
Then $|X| = n = 100\overline n$,
and by the previous paragraph,
Property (2) holds for $X$ with $\alpha = 1/101$.
Let $q$ be the minimum, over all elements $e$, of the number of sets in $X$ that contain $e$. So $X$ satisfies Property (1) for this $q$.
We claim that with positive probability $q \ge 80 \ln m$ (as needed for the lemma).
It remains only (i) to show this claim, and (ii) to argue that without loss of generality we can assume that, as stipulated in the post, $X$ is a set (rather than a multi-set).
(i) This follows from standard results about the integrality gap of the standard linear-program relaxation for set multi-cover.
But here is a self-contained argument:
Fix any element $e$. Recall that $\overline X$ is a fractional set cover. So, with each sample added to $X$, the probability that $e$ is covered is at least $1/|\overline X|$. So the expected number of sets in $X$ that cover $e$ is at least $n/|\overline X| = 100\overline n/|\overline X| \ge 100 H_m$. By a standard Chernoff bound, the probability that this number is less than $80 H_m = (1-1/5) 100 H_m$ is at most
$$\exp(-(1/5)^2 100 H_m/3) < \exp(-(33/25) \ln m) = o(1/m).$$
Now, by the naive union bound (summing over the $m$ elements $e$), the probability that $X$ fails to cover every element at least $80 H_m$ times is $o(1)$. This shows the claim.
(ii) Without loss of generality assume that no set occurs in $X$ more than $q$ times (otherwise simply reduce the number of copies to $q$; Properties (1) and (2) will still hold). Let $A$ be a set of $q$ new artificial elements. Modify $X$ as follows. Add all the elements of $A$ to every set in $X$, then, for each set $s$ that occurs more than once in $X$, remove a distinct element of $A$ from each copy of $s$ except the first. Let $X'$ be the resulting set family. By construction all sets in $X'$ are distinct. Property (2) holds for $X'$ because it holds for $X$.
For $X'$, Property (1) holds for each original element because $X$ has Property (1). Property (1) holds for each artificial element because each artificial element is in at least $m-d_2$ sets, where $d_2$ is the number of distinct sets that occur more than once in $X$, so that $d_2 \le m/2$, so that each artificial element is in at least $m-d_2 \ge m/2 \ge q$ sets in $X'$ (using here that $q = O(\log m)$). So $X'$ has the desired properties. $~~~\Box$