@VanCoding This got nothing to do with the Flatpak issues. I believe the issue you’re experiencing is due to insync-headless testing the real path of insync-headless executable so it must be running from /usr/lib/insync/insync-headless.
I also notice this because I’m maintaining the AUR package for insync-headless and wanted to not have it conflict with insync and installed under /usr/lib/insync-headless but to no avail. I reported it but this is the answer I received.
I personally will be moving my insync-headless installation into a container (Podman) as I only need this on my server and not in my base image so I lost the interest to nag the InsyncHQ about this.