While I can’t comment on the beeper side of things, I did look into matrix and bridges a bit.

From what I understand, for all e2ee services you use through beeper (and matrix in general), all messages get sent to the server encrypted by matrix, then the server decrypts them and they get re-encrypted in a different protocol (ie. WhatsApp/Signal/…) and then the encrypted message goes out to whatever service.

This would mean that technically the matrix server is able to read all your messages.

This is my main reason for still using the native apps for encrypted services. For unencrypted services I use a my own matrix server with bridges.