So far, here's what I've uncovered. I made tempfixes as I went. I'm going to make PRs now, and see what all these fixes get us.
Due to a bad bit of logic, Beaker isn't taking advantage of multiplexing. This actually isn't a significant factor though, because hypercloud shouldn't be using active replication anyway.
Hypercloud just isnt using dns discovery at all.
Hypercore-Archiver is emitting the 'add' event before persisting new keys to disk, causing archiver-server to join the discovery swarm prematurely. Beaker would connect and replication would fail.
Discovery swarm isnt creating one connection for each peer/discoveryKey combo. Instead, it's creating one connection for each peer. The connection would sit open and so nothing else would happen.
I have to confirm this still, but there were some signs that connections might be failing if they were initiated by hypercloud to my device running beaker. I want to get fixes 1-4 done, then I'll check on this.