Just had a bout of the game deciding to instantly CTD the second I started it through Steam, and when started directly via BorderlandsGOTY.exe it worked perfectly fine. So I figured since it starts the Launcher first, I checked everything out and looked in the save directory in the documents for launcher settings:
%USERPROFILE%\Documents\my games\Borderlands Game of the Year\LauncherData
Curiously, the launcher settings have no size. However, I simply renamed the LauncherSettings file as seen here to see what would happen if it had to regenerate the file. Sure enough, the launcher worked fine, and curiously skipped itself and went into the game, to which I was greeted with the FMVs I had turned off. So apparently this file controls whether or not you see the intro movies, but not whether or not the launcher skips directly into the game. And still curiously, the file has nothing at all in it. I’m bewildered as to how it saves anything at all or why this file was causing the crashes, but hopefully this helps someone out.
tl;dr if your game is crashing as you launch it through Steam, try regenerating the launcher settings file and make sure to turn off intro movies if you so desire.