I think everyone has their own preference when it comes to tuning a bow, and for most people, close enough is better than they can shoot.
I have come to the conclusion that I can't read paper holes well enough to get a perfect tune. I start with the paper, but then go to a bare shaft. I don't go crazy trying to make them slap shafts at 50 yards, but I use it as a check. Sometimes I get it right with the paper, sometimes it takes some minor tweaking. Once I get the bare shaft hitting how I want, I go back to the paper just to make sure something isn't lying to me.
The fletching will correct a LOT. But I've always been of the opinion that I would rather it not have to do any more work than absolutely necessary.
As for your other questions, point weight changes will affect the tune, but more than likely not enough for the average shooter to notice, unless you are really changing it a lot.
And the weight of the fletch does make a difference, but again, depending on the fletch you use (total weight), you probably won't notice.
I nock tune each arrow, and don't worry about what you are calling spine orientation. The problem with nock tuning to me is that it is a waste of time if you aren't able to shoot very tight groups. I buy good arrows and have had very few that didn't shoot consistent. Some may need turned so they hit with the rest of the arrows, but I have had very few that just wouldn't group.