I don't think so. The encrypted git functionality in Keybase operates differently from kbfs. AFAIK the encrypted git ability just functions as a git remote helper that doesn't use the local kbfs mount on your system, so you wouldn't run into the same situation as say a file you are copying to your private keybase folder.

Also, to be clear, you could use the mounted files directly, but you just have to be aware that if you lose connectivity you may run into issues. If I was traveling somewhere and I'd like to work on a document in transit then I would recommend copying that to another folder on your local machine first.