I don't think you can. The MapMFD looks at the list of bases on a planet's config file, and puts a marker at the coordinates.
I ran into this issue not that long ago. I sent up a rocket with a bunch of supplies (read that as UCGO base boxes) to the moon, and then the plan was fly there in an XR-2 and land next to it, unload the boxes, build my base, then do science, then fly home.
The rocket (a DM tug if memory serves) was assigned a Xpndr, but since it was a vessel, none of the MFDs that are useful when landing at a base could be used. Map MFD does not show landed vessels, only ones in flight. Cannot use the Xpndr as a VOR type of thing to approach. The workaround I did was to create a base at that location, and set up a VOR to act as the Transponder, and then use it that way. This method is not very appealing to the sensibilities I know, but it does allow the object to appear on the Map and then be able to make a more economical approach and landing near by.
the thing is, I just want to see it on MapMFD so when the Arrow does an alignment burn, the Crossrange when I turn on Autoland isn't huge. One solution is to leave a vessel with a transponder (like the Azure) and home in on that
Actually, you can get the UCGO's position from the scenario editor, and BaseSyncMFD can accept latitude/longitude as a target. Adding the Azure won't help - the Azure is "Landed" and won't show up in MapMFD.
I seem to recall that MapMFD won't target vessels that are "Landed" - only ones that are "orbiting".
Maybe you could contact the author,and see if he will update it for the XRs,you never know.Ah man, don't tell me that. XR2 is my primary means of space travel at the moment. Oh well, will just have to try it on something else then.

...Cannot use the Xpndr as a VOR type of thing to approach.

the thing is, I just want to see it on MapMFD so when the Arrow does an alignment burn, the Crossrange when I turn on Autoland isn't huge. One solution is to leave a vessel with a transponder (like the Azure) and home in on that