Ok, I just checked and they are indeed identical. main.dat section #5 and cgamain.dat section #3 are the same.
I finally solved the mystery. It contains the PC speaker sounds that play if you don't have enough memory to load ADLIB.DAT (but ADLIB.DAT is loaded before MAIN.DAT, so the game never works in that case).
Interestingly, I can't find any normal way to get the PC speaker sounds to play. They don't play normally, even if you don't have an AdLib-capable sound card. I was only able to get them to play by modifying the game to skip AdLib initialization. (Of course, maybe this is just a bug in the version of the game that I'm using. Edit: It was.)
Edit 2: There are 3 different versions of Lemmings for DOS with the VGALEMMI.EXE files dated 1991-05-10, 1991-05-24, and 1991-07-19. I was using the version dated 1991-05-24, which has a bug that makes PC speaker sound effects impossible. Incidentally, it also has the bug where the music starts over at track 1 every time you fail a level.
Edit 3: An easy way to tell which version you have is based on the message when you exit the game. If it says "Have a nice DOS!" then you have the buggy version.