The baseProductDir() contains the git branch name WebKitBuild/my_branch if that option is activated. The flatpak detection assumes that $baseProductDir/UserFlatpak holds the Flatpak data, that is no longer true within this setup. Let's think about how to fix this :-)
Created attachment 396072 [details] Patch
Committed r259864: <https://trac.webkit.org/changeset/259864>
<rdar://problem/61577164>