I'm in roughly the same boat as you (minus the multiple instances). My personal Minecraft server I run on a machine sitting behind me at home for friends uses SRV records. I bump the port number each "major" version release (yeah, I know, "minor" version in semver semantics) in case I ever have to run a previous version for whatever reason. This gets reflected in the SRV records. I've never actually had a reason to do this, but it's there if I need to.
Or at least that's the theory. I haven't updated it for 1.18. Not sure I will unless I run Tekkit or something in the future.
He’s scanning IP addresses, not dns names, so there’s no easy way to get SRV records. He could first do a reverse DNS lookup, but that would slow things down tremendously and also there are many, many Minecraft servers running without DNS names