Short Answer
The encoding doesn't seem to affect the problem's complexity.
Longer Answer
By changing the encoding, you are varying how the input size for the problem relates to the alphabet size, the number of automata, and the number of states per automaton.
If $c$ denotes the alphabet size, $k$ denotes the number of automata, and $m$ denotes the number of states per automaton, then under all reasonable encodings that I can think of, the input size will remain at least $max\{c, k, m\}$ and at most $p(c, k, m)$ for some multivariate polynomial $p$.
Therefore, using the typical PSPACE algorithm for the DFA intersection problem (along with potentially translating the input encoding) will still use at most polynomial space in terms of the new encoding's input size. Similarly, the typical reduction for PSPACE-hardness will still yield a polynomial sized input for the DFA intersection problem under the new input encoding.
It follows that the new variant of the problem is still PSPACE-complete.
Unary Automata
This question could be more interesting if we consider Unary DFA's (or other special subclasses of automata). Unary DFA's are much simpler taking the form of "pans" or "balloons". Their state diagrams are essentially directed cycles with a directed path attached to them. A natural improvement to encode such automata is to just list the path length in binary, the cycle length in binary, and binary labels for their final states. Without many final states, such an encoding could be logarithmic in size instead of linear.
The intersection problem for Unary DFA's is NP-complete as seen by related results in Meyer and Stockmeyer (1973) and Galil (1976). So it might be interesting to ask whether the encoding for unary DFA's affects the problem's complexity. However, as far as I can tell, even though the encoding can sometimes greatly affect the size of each automaton, it doesn't seem to change the NP-completeness of the problem.