While your Mac's display is being kept awake, macOS will not automatically switch from light to dark mode (and vice versa). Additionally, dynamic wallpapers will not change at the expected time if your Mac's display is being kept awake.
This issue is not unique to Amphetamine and affects all apps and processes that apply a system power assertion to keep a Mac's display awake. You can test this by running the following command in Terminal.app:
If you would like macOS to continue switching between light/dark mode, or updating your dynamic wallpaper on its regular schedule, regardless of whether your Mac's display is being kept awake, please submit a request to Apple: