Just so I understand you. You would rather do code changes on 94 files than look at, via the update process, compare/merge code conflicts in 10 or 15?
Have fun with that!
No. You don't seem to understand. What I suggest is what Highway of Life actually also posted a little later in this thread (although you seem to have misread that too). To use the Automatic Updater on all the files where the changes doesn't generate conflicts - then use Code Changes to update those 10-15 files. That does "require" those Code Changes to be available though (Yes you can use the patchfiles, but that is certainly a level higher in difficulty and risk of error for most).
But if you are asking me whether I'd rather do manual code changes on 94 files rather than try to figure out 10-15 files using the tools the Updater makes available to me - yes it'd be faster to do the 94 files of manual changes. Now when you add in patch files and diff/merge programs to help with the conflicts that changes and this changes to the situation described above. But having the Code Changes would be even more effective for those 10-15 files.
You can't guarantee the ability of everyone to update modified boards of course. At some point you risk having mods that are just incompatible with a new version or that require pretty large rewrites of files to work that is simply beyond a person with too little PHP skills to figure out. That's a risk you take when you heavily mod your board without having enough knowledge. However, you can do more or less - and providing manual Code Changes are a great asset for those with little knowledge of PHP. Often you can figure out how to move specific code up 5 lines to make it work or similar, even when you would have no idea about what the hell to do to merge two different files. Handling a specific line of code is much easier mentally than grasping the totality of two different versions of files of a program you didn't (and couldn't) write.