- Edited
troymccann after taking a quick look, I'm unsure whether there's any solution to the problem. The extensions just cannot work together at the moment.
This is due to Nightmode not being designed to handle multiple frontend groups, which is a very obscure feature only used by Flarum Embed extension and my own WP Embed. This means there are two different CSS files, but the code from Nightmode assumes there can be only one, and it replaces multiple style tags with the same target URL, which ends up being the file that contains just the WP CSS.
I will try to take a deeper look and will probably open an issue to discuss this on FoF Nightmode. I hope there's some way to disable Nightmode on custom frontends, but that's not looking good.