As far as I can see this has been changed more than a year ago already, I have not heart of any issues linked to this so far, so for most of the users I think it’s not relevant to have it set.
This is a dependency for snapd, that is also a dependency for manjaro-iso-tools-git. Have you installed/enabled snap-support, or manjaro -iso-tools-git ?
One disadvantage is the risk that several package versions remain on the computer in partially unmaintained versions but this issue can be addressed by encapsulation in a Sandbox and restricting the access to system resources. Furthermore, there is the potential issue that flatpaks could be enriched with addware and spyware in the future, since only the respective provider has control over the binary package. Massive criticism of flatpak is presented on flatkill.org.