Per my post here, MSIX packages need to be able to pass command line arguments to executed apps. This is presently not possible. Without this capability, my ability to package legacy apps with MS...
TaylorBrown Hopefully Microsoft will allow what you asked at some point.
Until then, I updated the Package Support Framework to allow what you need.. The updates this week would allow you to replace the target of your current shortcut with a copy of PsfLaunchXX.exe, and then edit the config.json file to launch your target exe with command line arguments specified in the config.json.