Duh, I figured out the mystery…
The reason was the wp-clone archive, which would transfer-over all the ARQ backup files. I adhered to your tutorial and turned off PF and ARQ before creating the archive (I even turned off BPS on top of that), yet for some reason those backup files were still all there.
And the reason the file count was larger was because it still had a theme in there that was not existent anymore in the current wp-clone archive. So basically
1. old theme present, ARQ-backup being created
2. old theme deinstalled, ARQ deactivated – backup still existent
3. wp-clone archive created and transferred to new site
4. restored on new domain but old ARQ backup still existing (360 files)
5. in ARQ dashboard deleting backup and creating new backup (where that old theme is not existing anymore) = 260 files.
Tada!
I guess I have to create a new wpclone archive with the bps backup folder completely deleted, as well as the plugin and I just install the plugin from scratch on all new sites. I find no benefit of cloning it to new sites because it needs to be deactivated, deinstalled and re-installed anyway, deleting all settings etc. and thus making it pointless to clone it over to new sites.