There is still gameplay after the final boss in at least years 1 and 2 (don't recall for 3 and 4), so I feel like it would make more sense for timing to end when the final cutscene plays

I agree, Year 3 doesn't even end with a boss so timing is especially jank. The main issue I find with this is that there is now no way to get the correct times for any previous runs, especially as the ones with video for Year 1 have a small delay going there, or don't end the chapter at all.

With year 1 it's a straight line iirc, so theoretically it would be easy enough to just add however many seconds it takes to run in a straight line. For year 2 and 3 I'm still the only runner, and I just set a new time for year 2 timed both ways, and my year 3 time is really bad so I should be able to improve that even with splitting later at the end. For any%, I'm yet to do a year 4 run so I'm not sure whether that would be easy to convert.