Didn’t know it only applied to UWP apps on Windows. That does seem like a pretty big problem then.
I don’t still have a Mac readily available to test with but afaik it is any application that uses Apple’s packaging format. It could also be that it needs to be in the “Applications” folder, but I’m almost certain it isn’t an App Store exclusive feature.
I use refind also, there should be a setting somewhere to let refind scan entries from other EFI partitions. I have that setup and just created a second EFI partition for my Linux setup, so that Windows has no idea Linux even exists. I even have everything running off of the same drive (my laptop only has one nvme slot) and I haven’t had any issues.