It knows you have a TBR, because of the OTBR integration, but if can’t see the mDNS announcements (required for discovery) because they are blocked by the router separating the two servers. This is one case where an mDNS reflector on the router might actually solve your issue (assuming you have ULAs and not just LLAs on the pi vlan).
It’s actually not a requirement that HA “see” the TBR, only that the credentials get synced to the mobile app for commissioning. Another option you might test is direct commissioning via rhe Matter server web console, but that requires setting up a dedicated Bluetooth radio for the matter server container, and keeping the new device within range of the server during setup.