Assumption: same route, speedrun check player control rather than hardware price.
Consider https://www.speedrun.com/mcm_d2/run/zx4qo4ey . Using IGT is bad cuz e.g. the running near 5:00 effect the gameplay but don't count in IGT; Using RTA is bad cuz e.g 6:00 doesn't effect the game and is strongly related to computer.
Please give us a better suggestion. Like seriously, we really want one.
If it really looks like the framerate drops to like 10fps at points then runners need to get some better hardware, or try to find out what they can do with their current system to make it run better. Minecraft games should not require beefy hardware. Also Autosplitters might help with removing loading differences. Also this is a HACK game, and that can come with lots of issues such as you pointed out, the in game timer not working right. At 6:00 the IGT (I assume) shows 2:59 so that is hilariously off so don't use IGT. RTA is probably your best bet.
This isn't really something you can make a general statement about, it very much depends on how the in-game timer is implemented for a particular game. But even then... okay? Neither method is perfect, unless you have an alternative in mind that's not really a useful thing to randomly point out.