Curious about this as well. Since Beeper uses bridges to communicate with other networks, (Signal, Whatsapp, Facebook, etc) and it needs to decrypt the messages before sending them over these bridges it is inherently less secure than using something like signal directly.

Beeper is just matrix with a bunch of preconfigured bridges for you. I've deployed a few of their bridges (as they're open source) for my own matrix server and can confirm they work perfectly.

Haven't had whatsapp installed on my phone for over 2 years. I even support the devs via github sponsors, I'm that happy with their bridges.

If you're not technical but want the benefits of bridging other networks into Matrix, Beeper is a great choice.