Mystery Gift Database appears to be missing...

[Sakress]

It appears that some Pokemon that work in PKHeX are marked as illegal. It makes it difficult to inject anything other than regular Pokemon. Also, I read there was supposed to be an illegal mode for injecting Pokemon marked as illegal? Where in the application is that found? Also, a cool feature to add would be the the Smogon importation tab and giving a GUI to Poke Ball selection.

[Larwive]

You were probably waiting for a very long time, I think a have the answer for your question :

How can I use the program to work with illegal pokémon?

Start the program from a command window with the "-hax" argument. Remember, you can be banned at any time for using illegal pokémon, and the ban can be permanent.

(From the Wiki)

I can't help you for the second part, I didn't participed in the conception of PKMN-NTR.

[TSRBerry]

The pokemon from Mystery Gifts were marked as illegal because the Database wasn't loaded on startup. I fixed this issue in my PR but the dev seems to be inactive.

I don't really understand what feature you would like to have in PKMN-NTR, but it would be awesome if someone would explain it again to me.