Yeah this is why I'll never view Signal as a real Whatsapp replacement. It fixes some of WA's issues but not many. There's still no federation and the ban on third-party apps makes it very hard to connect it to anything else.. I want fewer chat apps, not another new one alongside everything else :)
The mautrix-weechat bridge to Matrix uses the actual production Signal desktop client so they don't block it, but it's super wasteful because of this, it uses almost 1GB of memory just to relay some messages :P And it also uses your phone number as ID, doesn't allow integration with bots like Telegram does do, etc. It's ok for a small niche of people needing super secure chats but it's not the be-all end-all chat app.
So I recommended everyone around me against Signal as a Whatsapp replacement.. We should move to something that is solving all the problems, not just some of them. I think it's crucial that the network itself is just as open as the software, otherwise Signal can be sold and we end up with the same mess as Whatsapp once more (remember Whatsapp actually used to be a pretty decent IM app before Facebook took it over). Open protocols have been the building blocks of the internet and this fragmentation is making it a mess.
I think Matrix is the way to go, I just wish they could simplify their E2E a bit.. Right now it's too much in the way in terms of user experience.
What is potentially problematic is not the usage of the same backend but of the same actual servers.