The issue is that `noarch' packages built on musl don't match the ones 
built with glibc.

You should use a different `hostdir` for `musl`, i.e:

$ ./xbps-src -m masterdir-musl -H hostdir-musl binary-bootstrap x86_64-musl
$ ./xbps-src -m masterdir-musl -H hostdir-musl ...

(to build natively for x86_64/musl)