There is no work around. You use them with Homekit or not at all.
Try port mapping tcp port 51827 (HomeKit) and udp port 5353 (mDNS which is used for discovery) so your docker container can discover stuff from its internal network and talk to the HomeKit devices. You should be able to do that by adding the following to your Docker compose file (you probably have the last line already since that’s for the Home Assistant web interface):
Even then, it might not work, as I don’t think you can do multicast over the Docker bridge. But it’s worth a try. If that doesn’t work, then you’re either going to have to move HA to a Docker host that can do host networking, get rid of Docker altogether, or pitch the FP2s.