I don't think this is true of serial port access. AFAIK, you could talk to a serial port in every version of DOS and Windows with no problem up until Windows 8. Now suddenly, with Modern apps, it doesn't work at all.
Microsoft should have created an app capability for serial port access. Microsoft allows my app to become a network server, to impersonate me using my network credentials, and to access random removable storage. I would say all of those could be more insecure than accessing a serial port, which hooks up to hardware I have physical access to.
Hang on; since serial ports are handled by the Microsoft class driver, rather than by individual device drivers, are you sure you can't just ask for permission to talk to the class driver and open it as a character device for in/out access? Maybe we're overthinking this and the capability is already in there via the serial driver's class interface. Screw talking to the device driver, you only need to talk to the serial class driver.