Mikrotik never tried to resolve DNS from multiple servers. If first one fail, mikrotik considers it as a valid response.
If you want to resolve specific domains through different server, you can use FWD entry. E.G.:
/ip dns static add forward-to=10.0.0.1 regexp=".*\.example\.local" type=FWD
This will forward all your
*.example.local queries to your local domain server with IP 10.0.0.1
That is a theory but
unfortunately this does not work with DOH right now. Mikrotik staff is aware (reported in [SUP-20565],
resolved in v6.48beta12*) and hopefully they will soon release fix in stable channel.
For now, you have to do it with dst-nat (same way as we did it in the past):
/ip firewall layer7-protocol add name="local dns" regexp="^.+(.*.example.local).*\$"
/ip firewall nat add action=dst-nat chain=dstnat dst-port=53 layer7-protocol="local dns" log=yes protocol=udp to-addresses=10.0.0.1
this will work with DOH because it completely skips mikrotik's DNS system (DST-NAT occurs before routing decision and the packet goes to "forward" instead of "input").
* edit: still not fixed.