My problem, as outlined in my first post, is that I use LaunchBox as my overall game launcher. It launches all my Windows games, as well as all my emulated games. I've got somewhere around 5,700 games in my database, and I'd like to use that platform to launch both Freespace games, without the need to go to a separate launcher to configure each game. I have "settled" on the two mods that I'd like to use (one for FS1 that includes Silent Threat Reborn, one for FS2), and I have no interest in updating to the latest build and whatnot.
So, I copied the mdline_fso.cfg file into two new files, FS1.cfg and FS2.cfg. Then I created 2 batch files, each one configured to delete whatever current msline_fso.cfg file that exists, and copy the appropriate secondary .cfg file and rename it mdline_fso.cfg, then launch the game. The batch files are located in the main game directory. To wit:
Launch Freespace 1 w/Silent Threat Reborn:cls
@echo off
cd data
del cmdline_fso.cfg
copy fs1.cfg cmdline_fso.cfg
cd ..
start fs2_open_3_8_0_x64_AVX.exe
Launch Freespace 2:
cls
@echo off
cd data
del cmdline_fso.cfg
copy fs2.cfg cmdline_fso.cfg
cd ..
start fs2_open_3_8_0_x64_AVX.exe
...and Bob's yer uncle. Each batch file launches either FS1 or FS2 using the appropriate command line options and flags as setup in wXlauncher, and I've set up my LaunchBox prefs to use the batch files to run the games. I suggest this method for those players who already use a frontend like I do, and would prefer not dealing with a secondary launcher.