"For example, if you send a message from Beeper to a friend on WhatsApp, the message is encrypted on your Beeper client, sent to the bridge, which decrypts and re-encrypts the message with WhatsApp's proprietary encryption protocol."
Directly underneath that they also say:
"Using native end-to-end encrypted chat apps independently may be more secure than connecting to them to Beeper"
https://www.beeper.com/faq#how-does-beeper-connect-to-encryp...