This has been on my mind a lot, too. You've explained it much better, and it's something that we need to think about as both plugin and theme creators.

One thing that can really stump end-users is if they don't know how their site was built, and what will happen if they decide to change something. That tends to freak people out, and they sometimes want to just start over and give up.

I'm not sure how we overcome that, when some of these issues are pretty nuanced and technical.