Oh that sucks. I have tweaked 3-4 core files in 3.1.x because it's simpler than finding / creating / waiting for an extension. Plus more waiting after core phpBB is updated and the dev disappears and doesn't update their extensions.
I've been using phpBB long enough now (14 years) to know don't just rely on any extensions, pick only a few and only the best. Over time most will not be updated even though the core files are.
As a result of your news, I'm definitely going to document my few changes very well for upgrade time
Long term it would be nice to have a more streamlined upgrade process for phpBB, one where you don't even have to upload/download files (similar to WordPress, where it downloads the file directly to your webserver during the process).