I don't understand the problem here. SRV records do work for subdomains. I have used them myself many times in different versions of Minecraft and server querying worked normally. It is also used by a existing public servers. Are you sure this is a Minecraft issue rather than a misconfiguration of some kind?
I will be trying to make a test really quickly and I'll come back to you.
Definitively not a Minecraft issue. This is my configuration:
SVR _minecraft._tcp.mc.[domain] 0 0 25585 cloud.[domain]
[media]A cloud.[domain] [server_ip]
Make sure that you have set:
Maybe that's the problem you're having. Both query.port and server-port should be set to the same value.