How is that going to work? User arrives at site, OS is set to dark, site is toggled to dark, so far, so good (assuming the toggle is smart enough to be set appropriately at this point).
1) User toggles OS to light, is your site going to switch back?
2) User toggles site to light, and back to dark to see what that does, now there's a persisted app setting. User later realizes they don’t like dark, toggles OS to light, and then has to think about your app's unique way of toggling it back.
To me, that's just unwieldy for very little gain. Why would I want your app to be inconsistent with everything else, other than a poorly executed dark mode?
While there’s a good chance you won't be using my current apps, I’m confident I won’t be the only one to reach a similar conclusion, so you'll likely have to get used to the behavior.