Solarmass synth-ruiner
I saw some discussion in the Budgie community about issues with how GTK does its checks for the dark theme flag. From that discussion, I understood that it checks whether the theme name ends in the suffix "dark". Plata uses "Noir" instead of dark, so that might be the cause.
Platano will use the structure "Platano[-compact][-light|dark]" for the names of its variations in order to deal with this issue, at least on the GTK side. I'll check with the Budgie folks to make sure I understand this correctly, as I'm not 100% sure.
EDIT: This won't fix the flatpak bundle thing, but it should fix the "proper dark theme support" you point out @Solarmass