That article's premise is that the Android security model is something that I want. It really isn't.

The F-Droid model of having multiple repositories in one app is absolutely perfect because it gives me control (rather than the operating system) over what repositories I decide to add. There is no scenario in which I wish Android to question me on whether I want to install an app from a particular F-Droid repository.

Reads like a cheap hit piece to me.

The section you linked in particular is a load of editorialized bullshit IMO. As far as I can tell the only legitimate complaint is that there is (or was?) some sort of issue with the signing methodology for both APKs and repository metadata. Specifically they were apparently very slow to replace deprecated methods that had known issues. However it's worth noting that they appear to have been following what were at one point standard practices.

The certificate pinning nonsense is particularly egregious. APT famously doesn't need TLS unless you're concerned about confidentiality. It's the same for any package manager that securely signs everything, and if there's ever a signing vulnerability then relying on TLS certainly might save you but seems extremely risky. On top of that the Android TOFU model means none of this matters in the slightest for already installed apps which is expected to be the case the vast majority of the time.

As far as I'm concerned F-Droid is the best currently available option. That said of course there are places it could improve.

Can you describe the threat model / specific attack under which... any of the supposed flaws on that page matter? (Most of the particular section you've linked appears to be about extra defenses that could be added, but which are unlikely to make a difference in the face of Android's TOFU signature verification on installed APKs.)