Just did a full playthrough and I didn’t do any of these.
I let the mutants live for now to save the historical items (I was hoping to get the other Marshall to help take out the mutants and maybe pay me a fair share for the info), I followed the engineer out of town and then failed at saving him on the road, I did not romance Raquel although I was really quite fond of her and I would say that we bonded quite well.
Slightly annoyed that AIDAN found me… Untrustworthy? Not entirely sure what caused my loyalty to be in the 40s, but I guess I was just a bit too independent and rebellious in my thoughts.
Also, both my gunners died pretty anticlimactic deaths. The Frenchie died in the roadblock mine, and the mercenary sniper lady instantly got shot when we engaged the ones who bought the engineer. Thankfully I did not have to pay them.
When I got to the final settlement (Borgas?) with the engineer I reported that I did not have the engineer, for some weird buggy reason, and then I instantly got hit by shrapnel from the explosion, which was a bit of a downer.
Love the game and the concept though! Definitely a fan, will see what other arcs can be found in other playthroughs. I really ought to try to do the opposite of what my guide tells me to, and see how bad that will make the trip.