I know this may sound like a stupid question, but what is the difference?

No question is a stupid question unless you already know the answer. Good question. I would tell you but I don't know either

Do you know what LRT means?

Because I am uploading a speedrun, and it asks the timing method, but I used an in-game timer? I was doing a challenge level.

A vote was recently conducted in the discord deciding if we would use a load remover to time runs. LRT is Load Remover Time and RTA is Real Time Attack. Since the run you are submitting is a challenge, and it uses an in game timer you would just submit the time as normally. If you want to do another category, or full game runs, make sure to either download the load remover from the resources tab, or enable it through livesplit.

We are planning on adding an additional Timing Method "IGT," which will just stand for "In Game Time" and this will include Challenge ILs, Bounty Hunter ILs, Super Stories, and other things