That's what I ended up for MemPa (described above). The idea is that I can't read binary sha256 output, and everything I know that can translate in hex can also translate in base64 leading to shorter secrets.

For the special chars, I chose the Safari way of encoding, i.e. I only extract alpha-numberics from base64, and add a "-" every 3 chars. This also improves readability. I assume that if Apple chose this way of doing, either they studied it and/or sites will conform to that.