short answer: doesnt affect IGT, but you should probably correct it anyway for different reasons.
solution: go to the steam betas for celeste and set it to "beta-1.3.3.0 - v.1.4.4.0 (FNA)" and see if that fixes it.
long answer:
for the sake of in-game time it actually doesnt matter compared to the 60fps timer, but the entire game and its physics are running at 61fps instead of 60fps, which does make a small difference in how the game feels (essentially the game is ever so slightly faster and therefore more precise at 61fps). this also ends up making a RTA difference, but again, IGT is unaffected, thankfully.
this isnt really that big of a deal on its own, but the worst effect of it is that the modded client runs at 60fps usually, so if youre running modded with practice tools on 60fps, and then do your runs on vanilla on 61fps, thats pretty bad since youre playing on different game physics which, at a high enough skill level, will definitely impact your ability to develop muscle memory and consistency.
you should join the discord linked in the sidebar for more active conversation, nobody really uses the speedrun.com forums
join the discord - check out the resources channel in there. ask any questions in the hat-speedrunning channel https://discord.gg/pTxvKv
if you only want to change a few buttons you can edit a file in the game files, you should ask around in our discord for information on how to rebind using game files. people are more active there than on the forums here