Personally, I think it'd be nice if you could self-host just the bridge instances and connect them with beeper yourself, so that the part that isn't e2e encrypted is running on software you can validate and hardware you control.

I 100% agree this would be a great solution. That's what I thought this page was going to be at first until I kept reading and realized it's just a config guide for the Matrix Ansible setup. I wish they didn't say "self host Beeper" on that page at all because self hosting Matrix has absolutely nothing to do with the Beeper service other than their devs built the bridges that they're showing you how to set up with Matrix.