Right, but we need to disconnect those issues to "divide and conquer" this whole story, otherwise it makes it harder to find possible concrete improvements.
so you can adjust a installation just fine, you can install features and plugins...
That dir above has for me a "features", "plugins" "configuration" and a "p2" dir
And those have the same meaning i think as in a normal install
Except that in the configuration dir we have also that "eclipse.ini.ignored"
I think this is also something that can be improved, but may require changes in multiple places: the read-only eclipse.ini file could be copied and augmented into a local eclipse.ini (not ignored). However, even if there is a local eclipse.ini, would the launcher read it instead of the global one?
I suggest you open a new bug about this part of the story ;)