I suspect my workflow is pretty close to yours, Eike, since you're the one that suggested it to me. :-) I use one Oomph-installed copy of eclipse per workspace, and I have one workspace per branch+project combination. I usually have multiple open at the same time.
I also wouldn't want to get spammed by irrelevant notifications, but I don't think that having focus is the criteria I'd use for determining if a notification is relevant. If a background copy of Eclipse is waiting for my input to proceed with an operation (it needs a password, a confirmation, or a disambiguation), I probably want to know about it no matter what copy of Eclipse it came from. I'd hate to return to a copy of Eclipse that I thought was installing updates in the background only to discover that it had been waiting for me to click "Are you sure?".
However, if a copy of Eclipse is just informing me that it completed some sort of automatic sync or finished an operation I probably don't want the notification no matter what copy of Eclipse it came from. I think that filtering notifications based on focus is the sort of thing I'd only want if Eclipse was already overusing notifications... and if we have strong guidelines for when notifications are permitted, that shouldn't be the case.