> that uses a tool that is not yet in mise registry

Yes, you can directly get tools from npm/pypi/cargo/github-releases/asdf-plugins/vfox-plugins without anyone touching the mise registry. The registry is just a convenient index of short names e.g. "[email protected]" maps to ubi:junegunn/[email protected] which will download the appropriate arch binary from the v0.56.3 junegunn/fzf GitHub release.

> if I want to provide a python runtime that is compiled slightly differently

The default uses precompiled binaries, but with one setting it can use python-build/pyenv under the hood, then all the pyenv env vars can be used to configure the build process.