I don't understand why the msfs 2020 is partly on 1 drive while the main program is on another?

Unlike a program, MSFS is a partial app. Windows 10 keeps apps in WindowsApps as well as “local” (MS) or “roaming” (Steam)

When you use the “move” app in Windows 10 settings, it will move everything off of the C: drive, but it will create a “system” drive on your target for Windows apps.