You can do it, I have Wireguard set up between my house and another house with mDNS and SSDP working between them too. The IP traffic flows between the subnets normally as routed traffic over the Wireguard link but uses EoIP over the link as well with bridge filtering.
EoIP with bridge filters are added here so only SSDP (good for things like UPNP/DLNA discovery for multimedia systems) and mDNS (many things including printer discover/Airprint, Airplay, Chromecast etc) get through and all other layer 2 traffic from each subnet is blocked - you don’t want DHCP leaking across to the other subnet.
You need to do this filtering on each end once you get EoIP working over the Wireguard link. You don’t need to turn on IPSEC for EoIP as it’d be redundant in this case. You’ll have to do some homework to figure out what filter options to add for other broadcast based discovery mechanisms.
/interface bridge filter
add action=accept chain=forward dst-address=224.0.0.251/32 dst-mac-address=\
01:00:5E:00:00:FB/FF:FF:FF:FF:FF:FF dst-port=5353 ip-protocol=udp \
mac-protocol=ip out-interface=EoIP src-port=5353 comment=mDNS
add action=accept chain=forward comment=SSDP dst-address=239.255.255.250/32 \
dst-mac-address=01:00:5E:7F:FF:FA/FF:FF:FF:FF:FF:FF dst-port=1900 \
ip-protocol=udp mac-protocol=ip out-interface=EoIP
add action=drop chain=output out-interface=EoIP
add action=drop chain=forward out-interface=EoIP
Also see my original post which extends this bridge filtering idea to allow mDNS relaying between VLANs without a user space reflector program like Avahi.
http://forum.mikrotik.com/t/mdns-repeater-feature/148334/179