Is it safe to use Signal via Beeper?

I'd be cautious of Beeper. I guess my biggest concern personally is that it introduces an unnecessary middle man, and its closed source and proprietary, so there's no way at all to verify any claims they make.

To be charitable, I do think their claim on re-encryption of messages through the services themselves is true, but I think the bigger concern here is that whatever messages you send/receive also go through Beeper and not only services like Signal/iMessage/WhatsApp, and I'm unsure if Beeper encrypts the data they receive, or what access they have to it/how they handle it. That's my biggest issue, as it would effectively make end to end encryption on these services useless if Beeper just had full access and could see all of your messages and any metadata, which is what I suspect is the case.

tl:dr If you have a high threat model, definitely do not. If you want a good compromise between privacy and convenience, go for it.

"Safe" is not really a binary concept so it's a bit more complicated than that.

Beeper is a forked Matrix app. As such, it subjects all of your messages to all of the vulnerabilities of Matrix, mostly being that it collects a ton of metadata on whatever server of your account (in this case Beeper) and also whatever other servers you communicate across. So it's "safety" is really dependent on whether you trust Beeper not to sell or leak that info. They will definitely cough it up if they get a warrant. Where Signal doesn't have this data.

So you're increasing your attack surface by basically creating a metadata archive of your Signal messages.

As for the security of your message content, Beeper will get the decrypted info from the server you connect to your account, and then re-encrypts it as a Matrix message, so theoretically they don't have any of that. Some people make a big deal out of this, as they will actually have access to your plaintext messages (duh, you signed their server into your account) but I don't see anything to indicate these messages are stored.

There is a spectrum across convenience and privacy and this leans toward the latter.

What is the "pain" you're experiencing? You having a hard time with clicking the notification every app sends you? Difficulty identifying their unique app icons? Must be tough.