Couple of minor points.

The "Unable to set debug log file" message that you get when you try to start a game that is already running isn't very helpful.

Whe I first saw this I had no idea what it meant and it took me a couple of goes to work out that I had clicked the game start button twice.
Suggest a "Transcendence already running" message or something similar would be a bit more polished.

Also
The Transcendence game folder has a 'Readme.htm' file and there is also a Readme file of the same name in the Transdata.zip file.
So extracting Transdata.zip into a Trancendence game folder gives the "Already got a Readme.htm file here... blah blah.. Replace...etc?" popup.
New modders won't know whether they need both so will have to stop and check, etc, burning up time and creating uncertainty. Plus it is just another unnecessary thing to do every time you extract Transdata to the game folder.
Suggest that Transdata 'Readme.htm' file be changed to 'TransdataReadme.htm' so both files are available to modders (or people just having a look).