There is no completely free software, even if you take out the Intel ME (which is a very bad idea as it'll leave you super vulnerable) The Intel chip will never be open source or FOSS at a hardware level. Even RISC-5 being open still has trust issues. Unless you setup a chip fab you're at the helm of someone. And as the closed source hardware runs the open source software, is it really free?
A prime one is that the entity that you (have no choice but to) trust today will eventually turn against you at some point down the road.
using a 3rd party client is against Signal's ToS
As far as it being against signals tos, molly exists and had not received any problems from the signal foundation to my knowledge, discord has the same clause and they don't seem to give a rats ass. Sure they could enforce it but they don't, and personally with how matrix clients are handled they have mixed security, fluffychat has security issues ranging from outdated SDK versions to quite literally ddosing homeservers because of a non-existent rate limit.
pushing controversial features like crypto payments
The crypto stuff wasn't great but you know what's cool? You don't have to use it. Simple as that. You don't have to engage with it and you and I both know that. It's buried in settings and you have to find it yourself.
Signal is an entity that's incorporated in a jurisdiction and might be compelled by law or to degrade its encryption to comply with the local regulator.
Using a centralized service like Signal makes you an easily identifiable/prime target in such a scenario.
Signal is not an anonymity tool, and has never been advertised as such, if you need anonymity, signal is not a good choice. You can make it more anonymous by using a burner phone but that's a different topic.
No matter what Signal says, nobody but themselves can verify what code runs on their servers
As far as I understand the American law, any agency could tap into that, either directly, or via Amazon on which the whole thing is running.
If everything is encrypted, what could Amazon tap? You do realize sealed sender and PFS take away any trust from the server correct? It's all encrypted, your aren't trusting the server at all, it's completely trust-less, and unless you think Amazon or governments can at this very moment tap any encrypted data and decrypt it, I would recommend taking a walk outside and realize that no one, NO ONE can decrypt current encrypted standards.
Unless you can point me to a reputable article showing in great detail that signal is lying about their e2ee claims then I'll rest my case. Signal has been proven time and time again to not have any data on their users except the minimum required for the service to work, that's called integrity.
Also there will always be someone you trust on the internet, nothing will change that unless we completely rethink how the internet works.
Edit: added quotes Edit 2: added extra info
Freedom from what? Good security practices? Open source does not equal security nor freedom. You're pedaling digital politics instead of fact based privacy and security. Trust me I'd love my apps to be open source but ignoring blatant security issues is going to put someone at risk. You can't have privacy without security and vice versa.
edit: like I mentioned previously, use obtainium and you can still use open source software
It's only encrypted in a BFU state, (before first unlock). Police can probe your phone for data using a tool by cellebrite without root. GrapheneOS includes a auto rebooting feature to place it back in a BFU state but other phones will lack this feature. Using Molly's database lock allows you to not trust the OS itself by encrypting it.
edit: corrected cellbrite to cellebrite
Wdym anti features? The only thing fdroid does is take the developer APK, sign it themselves and release it. If any anti features exist (I assume you're talking about the anti features tab in the fdroid app) it won't make any difference where you obtain it as fdroid doesn't do code checks. They only check to make sure it's under a open source licence. Fdroid adds no protection to any apps and you trust them to ship clean packages. If you get packages from the developer and they sign it and it happens to be malicious it's only one app instead of all your apps you have from fdroid. You trust them a lot and I'd recommend reading this if anyone is interested. https://privsec.dev/posts/android/f-droid-security-issues/
The main issue with encrypting the database using Molly's setup is you'll miss notifications and calls until you unlock, this might be able to be fixed using a different database encryption setup but as it stands it would be inconvenient for many.
I wouldn't recommend using fdroid due to security concerns. When you download a fdroid so it is signed by fdroid instead of the developer, what this means it's if fdroid gets hacked all your fdroid apps are insecure and can receive malicious updates. You also trust fdroid as another party in the chain, when in reality you should remove as many parties as possible. They also tend to host outdated apps with no updates in years. Use obtainium as it will pull directly from the developers GitHub page and will be signed by the developer instead.
Signal on the Google play store isn't FOSS but it facilitates the delivery of notifications to the user. The protocol itself is open source and notifications are handled securely even with Google play services on the phone. If you want a FOSS version, use the APK on their website, it has an auto updater.
Molly is only available on Android, as far as differences it is a hardened fork of signal with an encrypted database, what that means in practice is even if someone was actively probing your phone to try to gain access to messages they wouldn't be able to due to the encryption. It's very useful if you are an active target or you don't trust your phone os to play nice. I personally use it myself and really like it but in general it's not terribly different.
I don't see an issue as signal is designed not to trust the server. Signal also uses sealed sender and Perfect Forward Secrecy, which is something almost all e2ee messengers lack. What it means in practice is signal leaks very little if any metadata, if you leak metadata you give away details about who your talking to and for how long, etc. Examples might include talking with a suicide hotline, or a doctor, maybe a customer service agent at a company and for how long. Those details will give a lot away about you, even if the messages or calls themselves are encrypted. Matrix is not recommended for communication because it fails to properly hide metadata and actively trusts the servers. When you make a call on signal, as long as both users have "Always Relay Calls" set to disabled, your calls will be peer to peer instead of trusting a central server to facilitate the connection and trusting a middle man. What this means is since the connection is peer to peer you can leak your IP address to the user you're talking to, however a VPN fixes this issue.
I agree, the features apple does implement do tend to be more polished or at the very least not annoying to the user.
Like everything in life it's about balance, using too much foss software and hardware could put you in much more risk, while using proprietary software won't give you the control or privacy you want. Once again foss software is great, but it is not perfect and should not be treated as such.