Could you add the swapstereo option to the [mixer] section? Default =false of course.
Then it would be possible to run a special .conf file for titles that have reversed stereo and no possibility to correct it in the game or setup program, like Terminal Velocity.
Apparently this setting is only available in some builds for DOSBox. Here is a thread with more context.
https://www.vogons.org/viewtopic.php?f=33&t=95484