Yeah that would be ideal method really but since the ispconfig3 upgrades are a little brutal and overwrite almost everything you changed, you have to keep backup copies and diff them in case they've added something to the page which a backup&restoring of your modified file would restore back to the old copy.
So i did it my way only for easy upgrade reasons only.
Would be nice if the ispc team styled everything a little better.
What you did was good work Mike, could try chattr +i on your files during upgrade to prevent overwriting and see how it goes. I know it doesn't work on custom postfix main.cf as complains before continuing, i know coz i tried it.
For some reason ispc3 upgrade screws my postfix configs so i have to always back it up.
it truely needs questionable sections for upgrades like templates, each service and so on..