I'm thinking about retiming top runs (i.e. sub-hour and runs close to that) as a fun side-project and I want to know how the loads should be timed.

wdym? Loads are timed normally, they don't take them out

Like for In-Game-Time

Timing the load itself is going to be impossible, but you can approximate by timing from fadeout to fadein.

Yeah, and I think the main reason we just don't bother with removing loads is because it would require retiming every run because some loads seem to be entirely random

Loads tend vary by a few "frames" each time, but sometimes can vary but upwards of a second. Between consoles is an entirely different story, as some consoles naturally load faster than others.