In the settings the graphics changes the time too, i made a crapy video about that . So irl time is definetaly the best option, though the times are have to retimed because i dont think livesplit has Checkpoint specific split options.
Im not a programer but it would also help if we could somehow get our hands on the games source code(altought i dont have high hopes for that)
I noticed it too, the problem is that if we count irl time then if your game runs slower you have mutch smaller chace to get a good time. So it wouldn't really be more fair, than the igt now.
Edit: I did some "testing" and when my computer was overwhelmed (AKA, i opened ton of games and youtube tabs) in 1 minute the igt read 31:35 (31 seconds) When I wasn't overwhelming my pc in 1 minute the igt read 32:02 (32 seconds) so it seems like it doesn't difer that mutch depending on the cpu/memory usage.