I use AutoHotKey to make an Icon that when clicked, opens a little popup menu with a list of Bentley Programs to select to run. In the menu source, I have two items for MicroStation - one loads it with SS2 and one loads it with SS3.
However, in MBE (MicroStation Basic, not VBA) there was a function that can force MicroStation to read a specified CFG file when called. It might be possible to use that to load the CFG files live to get the desired result. I used it in my V7 workspace - I will see if I can locate it to share. I looked in the MBE help and did not see it, which now makes me wonder if I called an MDL function from within an MBE macro. Whatever the case, it would either work or not in V8 - I know I had it working in V7.