I've looked into this a little. I have run different VASSAL versions and used different VASL module versions. However, there is only one preference file for each module, which is used whichever VASSAL version you use, and whichever VASL (or other) module version you use. I've never found a way to change the preference file.
I was thinking about writing a Python program that would allow you to specify by directory which VASSAL version, which module version, which extensions, and which preference file to use. (It would accomplish the last by keeping copies of the preference files for each module, under different names, and copying the right one to the common file.) Users would have to change the program associated with .vlog and .vsav files to the Python program. Besides letting you play old modules, that might need old versions of VASSAL, it would also allow you to have different passwords. That way, if you're playing in an online tournament, you can reveal your password at the end to let your opponent/the referee check your HIP, and you wouldn't reveal any other passwords because the one you revealed would be unique to that game (actually, directory). Is there any interest in a program like this?