The way that the autosplitter works is that it starts when the hidden ingame timer starts running (right when the first cutscene starts), and it splits when the game objective meets the objective that has been specified in the autosplitter. This is generally the objective that pops up on screen. There reason why we did this is because it's an easier way of implementing an autosplitter than searching for all of the mission memory, and because it can be very flexible at when certain points. The disadvantage is that the splits are a bit later than is conventional, namely just after the mission that you wanted to split on, and that some missions can't split because the objectives are the same (A Bad Crowd and Homeward Bound share the same objective, something along the lines of "Kill goths"). This takes away the possibility to split for that mission.

If you don't want to split on a certain mission, in Livesplit go to edit layout, double click scriptable auto splitter, and untick the boxes of missions that you don't wish to split on. A more drastic change is just taking out the mission in the autosplitter script completely.
If any other changes need to be made or if you have any suggestions, I respond reasonably quickly on Discord. If you come across any bugs, it would be nice if you would report them to me as well.

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Edit (2018-08-05):
The autosplitter has been updated with a load remover and the final split is now made at the loading screen before the final cutscene. Loading is detected in a rather primitive way, namely hints displaying in a specific memory address. This is detected with a list of hints that was obtained manually, so some hints might still be missing. However, this will be a very small percentage of loading screens. If you come across a hint where the loading isn't removed, please report it on discord.
Right now the removed load splits are only for research of what impact gear has on the speed of loading. It would be greatly appreciated if you uploaded your splits or also displayed a loadless timer on screen next to the RTA timer.