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Funny you guys are talking about this. I just finished a new commuter build (single speed pinnacle dolomite with an eccentric bottom bracket) and was just trying to figure out the best way to fix a rear flat.
Pretty much was going to do what you suggested with fix it whilst its still on. But would still like to be able to take the wheel out and fix what I need to on the side of the road if I ever needed to. Was trying to figure out a way to do all of this without messing with the EBB/Breaking the chain but I'm not too sure there is a simple/easy way to do so.
With track ends you learn how to fix punctures without removing the wheel pretty quickly anyway, disc brakes n mud guards, or not.