You can do custom modifications you just have to make sure you do proper documentation. That way if you upgrade you can put the custom modifications back in place. By the way, the auto upgrade can be set so that it will not overwrite files that have been changed.
The way I use to do it in Dolphin is that I would apply my custom changes to the upgrade files that way they were be applied at the same time I did the upgrades. I am uncertain how manually updating works in UNA and haven't been able to get any definite answers.