As you correctly stated, my dislike for the pkg_* tools is probably without merit here and based on incorrect assumptions. I'll make sure to learn about the OpenBSD variants.
The ports tree.. Well, that's what I'd like portshaker [1] for. Yes, you can do that manually, but it's a pain.
Bumping ports: Same for FreeBSD, but unless OpenBSD has a much more responsive ports teams/mailing list, this won't usually work fast (I know, I'm extrapolating again). I have currently a meager list of four ports in my overlay that currently don't exist in FreeBSD or are outdated, but these exist for quite a while now ("weeks"). I try to be a good citizen and submit these things upstream, but I don't like to depend on someone having commit access.
1: http://www.manualpages.de/FreeBSD/FreeBSD-ports-9.0-RELEASE/...
I just felt that your knowledge is seriously outdated or not based on actual usage of the OpenBSD tool (which, by the way, has had a steady stream of improvements throughout its existence). And it looks like I was right, if your experience is indeed based on FreeBSD & NetBSD. OpenBSD has its own tool, which was written from scratch on and for OpenBSD by Marc Espie. It is not based on the code by Hubbard. It is not at all the same thing the other BSDs have.
As for your own ports tree -- well, I can't tell what is the best method for your scenario; I primarily use the binary packages (and sometimes compile things outside the ports tree). But the most obvious thing to do (which I've done) is to checkout the official ports tree, add your own ports and/or make your changes in it and use it as such. You might have to merge upstream changes if they've updated something you have touched. But if you want to track the official ports in addition to your own, then it makes all the sense to watch out for overlapping updates, no?
Also, if you're bumping ports because the OpenBSD porters haven't done so yet, it might be a good idea to send the diff to ports@.