Nico,
I had the same concern, but after some testing, it appears the directories referred to in C:\Users[username}\AppData\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe are a file system link called a Junction. This means that any thing "written" to these directories is actually written to another location to where the directory is linked (in this case, D:\WpSystem[usernameGUID]\AppData\Local\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache\Packages. The files are not written to the C:\ drive.
Because you specified the D:\ drive, all the files do indeed go to the D:\ drive. I recall reading something about Microsoft Store apps that they MUST reside on the same drive as the Windows OS. With hard links, junctions, and symbolic links, this can create the appearance that MSFS IS installed on the OS drive while still allowing you to store the data files on another larger drive.
Hard links, junctions, and symbolic links have been around for a long time with NTFS and Unix/Linux. They just aren't commonly used in everyday applications. I'm including a link to more information below if you are curious about what they are and how they work.
Hard Links and Junctions - Win32 apps | Microsoft Docs
In any case, If you selected the D:\ drive in your initial install of MSFS and allow the default directory to be used in the MSFS install manager, you'll see that during the package install, the free space on your D:\ will shrink, not the free space on C:.
I hope this helps.
Cheers and happy flying!
Brett