flatpak: use /var/run/host/etc for flatpak sysconfdir

To ensure system flatpak installations can be seen.

Fixes #1125
2 jobs for master in 31 minutes and 23 seconds (queued for 2 seconds)
Status Job ID Name Coverage
  .Pre
passed #555180
flatpak

00:29:07

 
  .Post
passed #555181
nightly

00:02:15