This has worked just fine for the modding community for the past...almost decade? Maybe more. I suppose the popularity of Skyrim and the introduction to the modding community via Steam has caused a rift between the ideals of some of the newer community members and the older ones.
Pretty much spot on. The community is evolving and it's become easier to mod as well as there being a larger amount of users exposed to it. People won't always agree with someone's ideas or additions to mods (using Arthmoor's Oblivion gates in Open Cities or the chest/book/companion additions to WATER awhile back as examples) and given there are legal, acknowledged ways to make modifications without consent it's going to become more of an issue if modders don't want people removing or changing things through patches/esp mastering and something like a modder's version of the GPL is going to have to be drafted and used.
Courtesy is a nice thing, but if someone's stubborn and refuses to change or allow you to make a change and there's a legal way to do what you want to fix their program/mod/resources/what have you, there's no reason not to outside of others possibly seeing it as rude. Don't forget though that this could cause problems in the long run like in the example from earlier where a modder disappeared and if whomever it was that wanted to fix the bugs couldn't get into contact with them and it was under a license disallowing any sort of modification under any means (if that's feasible) then it'll just have to be shelved and hopefully someone will make a new mod with the same ideas and purpose on their own.

Down a ways in here -> http://wryemusings.com/Cathedral%20vs.%20Parlor.html
I think you are right on with the guesses. Some things like that I think should just remain as personal mods if the case came down to it.