There is the Modify course in which Paul goes deep into each modifier:
https://cgcookie.com/courses/course-modify-a-complete-guide-on-blender-s-modifiers-84c3c6a66db79804
But what you describe is just how things go, it’s just realities, even though realities are uncomfortable we deal with them. It’s like owning a house, you’re gonna have to do cleaning all the time and maintenance. I wish I didn’t have to do it, but we have to do it, it’s part of the fact in owning a house. Meshes and working in 3D also have it’s uncomfortable things to deal with, and we deal with them. It’s as simple as that really. That’s why we plan ahead. For example, know that if you’re going to use instances, be sure to know that it’s on objects that will benefit you for the changes to propagate, like a screw or a door handle. if you know you need variation, then you know you have to make a duplicate instead. And so on and so forth.
