For example, with Notepad++ you can right click a file and you see an "Edit with Notepad++" item. Because these context menus items are added via registry (and the MSIX container-izes it), the OS is...
alexmarin89 yes, I absolutely understand what you're saying but it's not addressing the issue. Let me choose a different example - let's say https://mediaarea.net/en/MediaInfo as the example. MediaInfo is a program that can open a video file and give you various details such as codec, bitrate, etc.
In this case, I wouldn't want MediaInfo to be the default program to open a video file (as obviously playback would be used more often). MediaInfo's installer adds a right-click menu option but this is not supported by MSIX. While your file association workaround would absolutely work for some programs, programs like MediaInfo need right-click menu support for best usability.