RE: Peep Tubing........
I put a tube on last year for all of the reasons you listed, but after however many shots it started to crack and eventually broke. I also had it catch on brush.
As far as peep alignment goes, you have to be careful the first couple hundred shots off a string for stretch and twist, but after that they generally are pretty consistent. I also check it when I put my arrow on the string. I don't know, just what I am used to and what I like I guess.