Well, I disagree with your disagreement. Part of the value of F-Droid is that the main repository can host packages that are vetted and maintained by uninvolved parties. Second, if the Matrix-run repository does reproducible builds, then... there's no problem. (That's the nature of reproducible builds.) Third, F-Droid was conceived to be distributed and decentralized. That's why it allows you to add other sources in the first place, there's even a feature baked in that lets you get/share apps (including F-Droid itself) in-person with people around you, and under the hood the whole thing uses a DVCS-style model where the package index is "dead" data and your device manages a copy. Fourth, an app author choosing to run their own repository means that they're invested in F-Droid, moreso than instances where F-Droid's role is to achieve "mere availability" for the package.

What's more, this incident is evidence that we need more decentralization, not less. In instances where decentralization is either already working or is up for consideration, we should encourage it, not try to eradicate it.