It would be really nice if Unraid had a method to generate certs for HTTPS and I could manage them natively. Dockers tend to want to use ports 80 and 443 which is already in use by unraid itself, and piping it to br0 and assigning the docker its own IP seems to break the letsencrypt docker.

You're probably running into the same thing I am. Once you assign your container to use br0 it uses macvlan and can't communicate over the network with other containers and the host.  It still works, like I can ping the piped container from a VM or from a PC on the LAN. 

 

One thing I haven't tried yet is giving Letsencrypt and another container you want to use with it both a second interface on virtbro internal network so they can talk over that, but still have external comms from the first interface.  I don't see a way to try it from the unraid gui but it can be done manually.