I developed a program to manage and launch different VASSAL configurations: combinations of VASSAL version, module, preferences, and extensions. It also lets you associate a directory with a configuration, so VASSAL launcher (VL for short) will use that configuration when you start a game file from there. It's available as a resource
here on GameSquad. It is written in Python, so you need that on your system to use VL.
In relevance to this thread, VL would let you have one configuration that runs VASSAL 3.7.16 with module VASL 6.7.1-beta4 and certain preferences and extensions, another that runs VASSAL 3.7.16 with module VASL 6.6.10 and difference preferences and extensions. You can also have directories associated with configurations, so when you open a game file from games\Fred it uses one configuration, and a different configuration for game files from games\Alice.
A README.txt, instructions, and the source files are in the .zip file.