Exe file working directory

This can be fixed with the help of the package support framework (aka PSF). This is a project microsoft launched to help fixup apps without touching their original codebase.

You can integrate the fixes manually, as documented in the github repo (link in the above mentioned article).

Or you can use the free Express edition (endorsed by Microsoft as you can see in the video) of Advanced Installer to automatically include the fixes, as show in this example video.

This support is available for free for all the fixups included in PSF repo on GitHub, it takes you only a few clicks to include the fixup in your package, without requiring any prior knowledge on how PSF works.

Since you already have an MSIX package, you can simply import that into a new project in the Express edition, to speed up the process, instead of converting your app all over again. You need to start from Import section, UWP AppX project (it also supports MSIX, but the GUI hasn't been refreshed yet)

P.S. Disclaimer: I work on the team building Advanced Installer, you can see more cool MSIX features in my recent Ignite talk.