I just noticed a new beta feature on github for creating fine-grained personal access tokens and ran a few tests to see if it would work with node-red projects. It does, but...
on https://github.com/, it is found at settings -> developer settings -> personal access tokens -> fine-grained tokens
I suppose it is for limiting access to specific repos, unlike the other tokens.
I was able to make a token for 1 specific repo with limited access that was just enough for pushing updates from a node-red project by selecting the repo and changing this single setting to read and write.
The difference for using it is a little bit goofy. in the little popup window for authenticating when pushing changes from the node-red project, the original personal access tokens could be entered in the username box or enter a dummy user name and enter the token in the password box.
The new token type can only be used in the password box and you have to populate the username with something.