I have been battling with these same type questions as I finish all these same type of details.
Here's where I have found myself: I want my car to look & present itself correctly. I am using as many original parts as I can & trying to install many of them in the correct way with the correct paints. But, some of the things that really bug me I am & have already changed. They are the details that would hurt in a concours competition, but Once I decided not to follow that type of restoration, it made it easier to continue and deviate from original where I saw fit. For me, its been things like no over spray on the floor pans or under hood, over restored & over painted chassis parts, etc. I am installing my door latches & strikes clean, with no overspray. I just like that clean look. should still look good just not "correct"
But I still struggle with what way to go with things. Today I was deciding wether to paint the front sway bar chassis black, or natural steel. I have seen them both ways & don't know what I like better. Leaning towards natural steel though
I also added a 70 rear sway bar. Looks completely correct, but of course wasn't even available on our cars. So, I feel your pain, but unless your car is going to be completely correct, I would't be afraid to change things that really bug you.
Ironically I did paint over my hinge bolts. Once I had all the panels fitting perfect, I removed the hinge pins & left the halves installed & painted them. Top pins have to be installed upside down with this method however.....