are you allowed to replace the game timer in the top left with your livesplit? (obviously im using the autosplitter, so the livesplit time is the exact same as igt) or do you have to have the in game timer visible at all times

You can if your livesplit timer displays the hundredths in the milliseconds (should be like that by default).

Just keep in mind that if you have in game timer turned off, the version wont show in the pie screen and whatnot, which is important for verification. One thing you can do for this is turn on the in game timer in epilogue before showing the pie screen.