RPM’s aren’t quite comparable. These include core system components that aren’t exchangeable between distro’s due to differences between those distro’s. Flatpaks are aimed at GUI user applications, which are distro agnostic. In fact, with a Flatpak future your RPM repo’s should see the removal of GUI application packages and become focussed on those core OS packages and CLI tools.
Why would more fragmentation be better? That fragmentation in both technologies (deb/prm/apk/etc. and now flatpak vs snap) been a massive gripe for vendors, developers to users alike for decades. Flatpak is THE opportunity to consolidate application distribution. Vendors and developers aren’t looking to CI/CD to numerous destinations. They prefer to have one. Users aren’t looking for multiple application stores or sources. They too prefer to have one that contains everything.
Hate to say it, but this sounds like FUD rhetoric from Microsoft’s proprietary glory days to me. I’m not even aware of any trust issues. Why not abandon your own repo and throw your weight behind Flathub? That would immediately resolve any reservations one might have, like trust issues with regards to the build system…
Have you considered that this might not be within your control? Vendors and developers all seem to settle on publishing to Flathub only. That means it’ll be up to Red Hat to add these applications to your own repository. It has 1150 entries already so small chance that you’re going to be able to catch up and keep up if nobody pushes anything and it’s all up to you to pull. Firefox for example is already better from Flathub than from your registry. Not a very economic way to spend Red Hat’s limited and expensive capacity. Especially considering the much more efficient alternative of adopting Flathub and throwing your weight behind it to remove any doubts around the reliability of its build system and add a feature to distinguish between free and non-free entries.