Got a very helpful and quick reply from Meindert Sprang at Shipmodul.
The 460800 is to support all inputs without data loss, hardware flow control supported but data is buffered, so it's not mandated.
On Windows and OS X the miniplex 3USB uses a patched driver which sets the baud rate at 460800. Consequently even of your windows / OS X app doesn't support 460800, the maniple's driver will ignore what the app is trying to set and use 460800. Your OpenCPN on windows and OS X should work fine with it.
On Linux it's a different story: Using the standard ftdi_sio driver you'd have to explicitly set 460800.
So where does this leave us?
Unlike some unixen (like OS X) Linux doesn't revert the settings on serial ports when they're closed so it could be worth a try to set up the serial port using stty: I haven't confirmed stty on Linux supports 460800 yet but I assume from Minder's reply that the diver does. So first thing to try might be to set up the serial port with stty then treat it like a normal file interface (as above). That won't work for bi-directional though.
Mean time I'll look at adding support for 460800. This might actually take longer than it otherwise would as I'm half way through a minor re-write which has started to get a bit more major than I intended....