Thread HA and VLANs - will this work?

As Wally mentioned, you’ll need to add Matter Server to the IOT VLAN as the Matter Server is also using mDNS. One other thing to figure out is that the OTBR, AFAIK, can’t be setup for static IPv6. It will send out IPv6 Router Advertisements that include both a prefix for the IOT VLAN to use and a route to reach the Thread devices, so the system running the Matter Server and will need to be setup to accept and process these RAs appropriately.