DMT which is installed by eCS2.1+ and run during boot also helps quite a bit in keeping cruft out of the ini files. I do find that it occasionally locks up here when running, probably a timing issue.
DMT definitely helps, but it is not a complete answer (I think DMT could be a lot more aggressive, but I am not an expert).
I haven't had it lock up, although that may be happening on one of my little used boot systems now. It stops booting at DMT, and I haven't had the time to sort it out, yet.
One thing that DMT does do, is confuse CLEANINI. If CLEANINI only prints a few lines, and stops, close CLEANINI, create something on the desktop, delete whatever it is, then, CLEANINI will do it's thing.