There are two issues at play here. First, VatSpy, the VATSIM website, and other 3rd party apps are reading the altitude from the “plane altitude” simulation variable, which is the airplane’s true altitude, not the pressure altitude. This has always been an issue when above the transition altitude. Unless the sea level pressure is 29.92, the true altitude will be different than the pressure altitude.
The second issue is that MSFS is the first and only sim that takes into account the pressure lapse rate with altitude. This means the airplane’s true altitude will take air density variations into account, so an airplane’s true altitude in MSFS will be different than an airplane’s true altitude in, say P3D, when both airplanes are at the same pressure altitude unless the pressure lapse rate conforms exactly to the standard day lapse rate.