Actually what would be best is an installer, which permist both options. There are cases where users are not allowed to make a system installation and where users are requested to make a per user setup.

What would be better?

@abhinayagarwal

1. Would it be considerable to offer 2 MSI, one as per-user and the other one as per-system installation for Windows?
2. Or would it be better to to have one MSI where the user could choose between system and per-user setup?

For option 2) we would have to modify the jpackage main.wxs template file. Out of the box jpackage only supports the one or the other, not both.

I can imagine, that as a short term solution, we could offer a 2nd MSI file.

I would be inclined to explore 2nd option and override the wix files to create an installer to create both of these options in a single installer.