Hello,
I think IPB should take a look in for Modification Code Edits as they should be kept intact while upgrading to new Version of IPB. As Admins take lotz of pain for code of Modifications on their Board.

IPS do not support use of modifications. All edits made to the code is your responsibility, and if you submit a ticket with a problem that could be related to a modification, they will either refuse to help you, or upload unedited files.

But they've done a great job with the new hook system, which allow 3rd developers to do almost everything without the need to edit files. And as they continue to improve the system, it is likely that you wont have to do any edits, ever.