alcaray: No that's not the problem. The problem is how drastic a change the developers had to make to solve any given problem. If they needed to make a change to the saves in order to make something happen, then it does not matter how the fix is applied... Unless the patch fixes the saves or if there is a save fix program or procedure. But even then, there are changes that might not be possible to fix. It all depends.
Obsidian was very specific at wanting to never break saves ever since releasing the game and every patch introduced retroactive fixes to saved games, so yes, whether those fixes are applied during the patching process or on game load is the main concern here.