You can try to understand what actual happens when you tick this checkboxes - meaning, does it change something in the registry or file, once understood you can deploy a PS script that makes that change and use that script as an install parameter for you win32 app (there are many examples on google).
Another approach you can take is instead of using win32 app, use MSIX - this will record the installation process including the change that happens when you manually tick the box (there some requirements to follow when using MSIX - all described on MS docs).
And finally, I would contact the software vendor, maybe they already have a solution for that, could be a simple installation parameters.
