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F-Droid installs an APK that F-Droid compiled. Obtainium installs an APK that the app developer themselves compiled. I'm not sure what you're getting at.
Malicious APKs, built by the developer themselves, not matching their public source code.
Which developer?
E: Lol @ the ninja edit.
That's hardly a meaningful advantage for f-droid and the whole man in the middle risk you're exposing yourself to there. If you don't trust the developer to do the bare minimum of providing a release that matches source then why are you even installing their app? Satyr's response about developers getting compromised has way more weight in that conversation, but still falls short IMO.
Making sure the apk matches public source and running it through VT aren't going to catch a malicious apk that has the nasty bits buried in various commits but checks out in VT and matches the public source code. Sure, it'll burn them as a developer if/when they get caught, but how often does the community truly do code reviews on one-off Android apps? Not often enough to catch that kinda thing before it spreads without getting insanely lucky.
If you think about it, any developer could have their account hacked and the attacker upload an APK that includes malware. Obtainium isn't doing any malware scan or building from source or anything. If you are planning to just install from GitHub anyway, Obtainium should be a no-brainer. But I can see where might argue that having a middleman like F-Droid to validate APK integrity has some merits.
https://f-droid.org/docs/Security_Model/
https://f-droid.org/docs/Reproducible_Builds/
https://apt.izzysoft.de/fdroid/index/info#security
Fair point. I guess it boils down to if you prefer speed of update (obtainium) or the extra checks f-droid has in place and if you continue to trust that f-droid's stuff doesn't get compromised.
It's also worth mentioning f-droid's workflow far from guarantees there's nothing nefarious in a package. The bar looks to be passing virus total and then ensuring the provided apk matches source. If nobody reviews the source each time then every release could be the one that gets a nasty surprise.