Now, I swear this is not just laziness speaking, but I think I prefer it without the template. Keeping the navigation wrapper from the site is nice (like Django does), but when I'm in a bug tracker I like to know my way around. To some degree I've started to feel comfortable in Trac (simply because it's become very common). I want consistency with other Trac instances, not with the site or project the tracker is attached to. The way I interact with a tracker has little or nothing to do with the project that uses it, and everything to do with the software behind the tracker.
I feel like there's some important user interface lesson here, but I don't think it's actually important enough for me to try to extract it. Plus that'd be pretentious. I'll say only this: hobgoblins!
I've felt the same way. The navigation in and out of trac instances, to the project pages, to the weblog is just wrong. I had a plan for that but... well... you know.