Hey b, I am in the learning process also, likely for the rest of my life!!! 🙄 I am under the impression that a jewel hole is put in to be able to withstand wear by a steel pivot. the jewel will usually not be the culprit but the pivot will as it is most likely to be worn. On the other hand pivot holes that are not jeweled would be subject to more wear but treated similarly for fit as the jeweled hole. one thing I can think of on this is to check the end shake and side shake of any given wheel pivot. I think anything more than 5 degrees side shake is too much, and the end shake should not be much at all yet perceptible. As David mentions, chips or cracks in the jewel is a issue and should be replaced as they will cause alot of wear. BUT if I understand your question, @watchthebear wrote:
The simplest question I can ask is: shoud there be any penetration of the pivot or pinion cylinder through the back side?
Checking the end and side shake would most likely let you know if you had a bad or worn pivot…..and this would be why is would stick out the plate more than others……A good book I am reading thru is the “practical watch repairing, by Donald de Carle” I do have another book on its way (I will wait to mention it until I get it) and guys on here have mention other books that are really good, explaining how to inspect a watch as you go thru it. I hope someone with more knowledge chimes in and sets us straight 
, Have a great day, William