Screenshots shouldn't be optional, and if dark and light themes are provided in the app, then show both. It'll help users decide to try out the app. In my opinion, a lack luster presentation will discourage potential users.
I do lean towards the guidelines being enforced. As a user, it'll give me more confidence in flatpaks.
Although I do not like a title of a statement with a question mark glued on. This is a pet peeve of mine. You could ask "is flatpak's icon style guide too strict?", though Betteridge's law of headlines says the answer is no.
The whole point of that is make it clear that the dark mode of the app isn't its default state. It doesn't say "dark theme bad", it clearly says just that the screenshots shouldn't only be in dark mode.
That dark theme screenshot is bad and light theme is good is nuts because if theme is important you provide a 50/50 screenshot showing off the themes.
I don't think that was the point, it says "Having some screenshots to show off that e.g. dark style is supported is fine."
If you look at the screenshot, it shows the app using a weird font, as well as non-default header bar buttons. That's the main area of contention. Screenshots showing weird fonts, non-standard window additions, custom themes, aren't recommended.
Showing the app supports dark mode is completely fine.