Two betrayals is horrible for this. After I took down the first generator I didn't get a single checkpoint for the rest of the mission.

I think it depends on the level and the techniques you use. I know when I played The Silent Cartographer and Assault On The Control Room, between the use of the double jump and the musket, I skipped several triggers on accident. Some triggers were just enemy spawns, but some were actual checkpoints. Levels like Two Betrayals however I found to be rather broken with checkpoints only working up to the first generator even without any launching/level skipping methods.

Desperately fighting for your life while crossing your fingers for a checkpoint is just part of the Halo: Combat Evolved experience. This mod only makes that more true.