No it didn't come with the plate and I forgot to order it, but I bet it won't be that difficult to modify the existing cover.
You can get some paint and get it to match your bike. Having the factory case mount does look great on the bike.
I was thinking about that, painting the black cover but it may be better to leave it black since the luggage rack is black. Black does look ok with the Blue.
If you looked at the cover that is pre-cut for that rack you'll see the hole that is cut is as large as the part of the plate that has the 2 holes in it. That is so you can screw in the bolts for those. And also when you buy the plate it comes with a rubber insert to cover the slot that is cut in the plate, like a large rectangular rubber grommet.
Will be interesting to see your end result.