Note that the UDA50 programmers documentation kit have several things in there, and even so it's probably not complete.
The basic disc handling have several subsections deleted. Basically everything related to bad block handling for example, is not in. DUP is in a separate manual, that was uploaded much later than the basic stuff.
And of course, this is all dealing with things at the MSCP and DUP level, and don't even go into any information about the internals of the UDA50, which you would need if you planned to write your own application for that controller.
And you are trying to do something very different than what DUP is there for. You want to hook into the MSCP functionality to serve a different type of disk on the floppy port. I should remind you that the MSCP server is still running, so you cannot just take over that piece. Also, those processes are owning the floppy port and controller, which you need to stop them doing if you plan to use that port. And then, of course, you need to have your application interact with the whole MSCP system. Not to mention that any OS still would probably be rather confused if presented with something like an RX01 on an MSCP controller, because that didn't exist.
And I don't even know if the system will properly serve MSCP fully while DUP is running something.
And finally, this documentation deals with the UDA50. As soon as you look under the hood, the RQDX3 is a completely different controller.