You can use nonstandard controls and still allow people to customise colours. There are APIs (GetSysColor for instance) which’ll let you query and honour user settings, assuming you care to and don’t put your branding / Look & Feel preferences ahead of the user’s.

The fact you can doesn’t mean apps do.

They probably fixed it now, but this is what Microsofts own explorer looked like in 2018 with Dark Mode:

https://www.howtogeek.com/fyi/microsoft-adds-a-dark-theme-to...

You can guess about the support in third party apps.

For comparison, Windows 98 dark theme:

https://i.imgur.com/jVM9dUA.png

Windows 98, when most apps still used normal widgets.

As an example these days the Windows OS includes Microsoft apps that are built using the QT toolkit (OneDrive). That’s the example developers follow.