New issue by pullmoll on void-packages repository

https://github.com/void-linux/void-packages/issues/18230

Description:
Here are the steps to reproduce:
```
$ ./xbps-src zap
=> xbps-src: /home/jbu/src/void-packages/masterdir masterdir cleaned up.

$ ./xbps-src binary-bootstrap x86_64-musl
=> xbps-src: installing base-chroot...
=> xbps-src: updating repositories for host (x86_64-musl)...
[*] Updating `https://alpha.de.repo.voidlinux.org/current/musl/x86_64-musl-repodata' ...
x86_64-musl-repodata: 1891KB [avg rate: 6696KB/s]
[*] Updating `https://alpha.de.repo.voidlinux.org/current/musl/nonfree/x86_64-musl-repodata' ...
x86_64-musl-repodata: 4443B [avg rate: 88MB/s]
[*] Updating `https://alpha.de.repo.voidlinux.org/current/musl/debug/x86_64-musl-repodata' ...
x86_64-musl-repodata: 801KB [avg rate: 32GB/s]

Name                Action    Version           New version            Download size
kernel-libc-headers install   -                 4.19.0_2               928KB 
…
=> xbps-src: cleaning up masterdir...

$ ./xbps-src -t -E -N pkg gcc
=> xbps-src: gcc-9.2.0_3: found (x86_64-musl) (https://alpha.de.repo.voidlinux.org/current/musl)
```
So the `-N` or `$XBPS_SKIP_REMOTEREPOS` is ignored with `-E`, yet I want to build only packages which are not available in my **local** repository.

The reason is there are `masterdir/etc/xbps.d/20-repository-remote.conf`, and `22-repository-remote-x86_64.conf` for `x86_64`, which are not removed or ignored when the package availability is checked. After manually removing the files everything works while that should not be necessary.
Anyone has an idea what to do to solve this?