Honestly, overriding profiles per repo sounds like a disaster waiting to happen for me. I'm pretty sure I'd check out a repo and forget to set the right identity for it at some point. But if it works better for you, it works better for you.
I'm curious: if you're not grouping repos in your filesystem according to which context they're from — which for me dictates which identity I want to use — how are you choosing which directories to store repos in? Or does the context not dictate which identity you want to use?