I have seen strange things from Gnome, imho its the most convoluted linux desktop. In the past I had a similar situation with themes.
As far as placing a theme in /usr/share/themes instead of ~./.themes, it makes little difference. All its doing is adding color. But perhaps /usr/local/share/themes would be a better place.
But getting back to the Kripton theme. Its not incompatible. Otherwise they couldnt load it in the first place, only to loose the setting on reboot.
To make sure I booted into my Gnome partition, updated it, and put Kripton v40 in ~./.themes. Enabled it as the legacy them in Appearance, and rebooted several times. The theme just worked.