they have the normal usecase in mind for testing and support. Special cases like yours with a dual boot and use folders like windowsapps twice, is just not in focus and its understandable “why”. I also agree with @MSFSRonS that this is not a MSFS issue in generall.
We , the community, can not tell you whether you can get your money back as these reason. I asssume not, but I’am just only part of the community ( as all the other users in forum too ).
I assume there are not many users which try your solution, and so there is possible not much experiance in case of issues. I not sure whether it might be a solution to install the game content ( this which is the big part ) onto a common folder ( not sharing whole windowsapp ). Just only the “packages” folder. May be the issue exist because you share also config files. But as said, its more guesses like knowing.
EDIT:
in case I missunderstood and you can not delete the files on E: because windowsapp system secure, then would be possible this topic interessting.