Ohh I like the logbook idea. I'm actually planning for the next patch to have bit of a more "saving progress" and unlocking things to be maybe used at the start of a new run. I'm thinking of allowing you to go inside your ship and tweak some stuff there for the start of the run from the stuff you've unlocked. The logbook could be there too I guess and it'd offer some hints/explanations you've encountered in a more lore way.
And for the initial cargo roll rigging, I'd more like a system that would incentivise you to keep trying even on a bad roll like the brilliant whale mechanic in Slay the Spire (gives you an additional item on start of a run if you reached the first boss on your previous one).
The angel/devil fights are supposed to be quite often too dangerous. That's why you get to choose whether to do it or not and shouldn't be just snap-challenged. It can take a lot of your cargo to succeed (or everything even and still fail) but on the flip-side the reward is also pretty much better than anything else in the game right now.