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.