Toxtricity has original nature restrictions for its evolution; double check that your original nature is correct.
I've removed the Scrafty/Scraggy HA ban in the most recent commit, ty for bringing it to my attention
Box unlock flags and badges aren't event flags, they're set elsewhere in the save file.
You'll have to dig around with HxD/etc to find what bytes are changing in the save data, and modify them to see if the in-game value changes as expected.
Unlike prior games, the gift's contents are instantly added to your save data.
You have to receive the gift naturally in order to get that screen. No save edits will allow you to see that screen.