I have made this guide, in both XLSX and PDF format, to help with excluding splits from the autosplitter. I have used my own current route as an example, but you may need to move the missions around for it to apply to your route if it is different.

The autosplitter can be a bit tricky to exclude splits from, since we are only able to label the starting missions, due to the rest of the missions not being linear. I.e., you can change the order of missions around at will. The game also counts some missions as more than one completed mission, most notably Path to Oros, Udam Homeland and Izila Homeland.

Here are some examples of how to exclude splits. If I only want one split for killing Ull instead of four, and I want it to split when I kill Ull, I have to uncheck missions 24, 25 and 27 in the autosplit settings. And if I only wanted the Prologue to split after the end of the swim, I would uncheck missions 1 and 2.