Ok so the way I've done it basically involves the following:
When I install Windows App Support, it also installs bottles. For the purposes of my sanity and keeping my system clean...ish, I'm going to use that for this example. So once you open bottles and install your program in a new bottle, we can then get to work (I installed version 4.5 of ADE without an issue).
Close Bottles.
Bottles that gets installed is a flatpak, and as such we need to allow it to create desktop entries for the program that's installed, which we can do by the following:
flatpak override com.usebottles.bottles --user --filesystem=xdg-data/applications
Once entered, we can open up bottles and go to our newly installed program, and select "Add Desktop Entry".
This won't actually create an icon (because Gnome funtimes and whatnot) however, the file we need is created in:
/home/yourNameHere/.local/share/applications
The file for ADE in this example is going to be called an easily rememberable:
ADE--DigitalEditions--1727831033.448434.desktop
After that, you should be able to see the option to open an item using the "Open With..." Dialogue
The current issue I'm facing is getting the file to open properly. It currently brings up an error stating the file name is too long. This makes sense, given it's most likely passing over the full drive letter path since it's not exactly in the same drive. I'm currently looking into that issue.
I was sure that this was how the system would work by default, but maybe i'm on some coocoo pills. Will report back once I figure out the file path too long issue. Unless someone here has an easy solution to that that I can throw into the desktop entry file