I don't believe the technical details are as significant as the
systemtic change to the boundaries of trusted software maintainers.

Consider this comment, which appears to be the core justification:

Michael Catanzaro wrote:
> 
> Flatpaks already take precedence over RPMs, and there are no plans to
> change this for the reasons I mentioned in my previous mail regarding
> sandboxing, which is more important than other considerations.

A sandboxed trojan application is still capable of damaging the user's
security, even if it can't damage the system's security.

To illustrate the difference, a subverted browser can share all credit
card details seen (user's security compromised), but removing that
software removes the subversion (system security not compromised)

A preference order of

  Fedora Flatpak > GNOME Flatpak > Fedora RPM

makes user's security of graphical applications reliant upon a wider
set of trusted software maintainers than

  Fedora Flatpak > Fedora RPM > GNOME Flatpak

Essentially, for graphical applications the change makes Fedora trust
and security processes approach the minimum of of Fedora trust and
security processes and GNOME trust and security processes. That's 
change to the security stance of the distribution which requires
explicit discussion prior to accepting the change.

-glen
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