Problem is, you have to launch it in Classic Mode for the Sky3DS to work - since it shows up like an actual game card, it doesn't use exploits or anything to run (which is why it works on anything currently)
And that makes it have the exact same problem as using retail game cards with SaveDataFiler... that you can't use installed CIA files in Classic Mode.
So to answer your question - no, I haven't tried it, but I'm 100% sure it won't work until Gateway/MT stops requiring flash-card mode in order to use installed .cia files.