I think DesktopGL MonoGame uses SDL for input whereas DirectX uses DirectInput, apparently these means DesktopGL has much wider controller support. So I’ve heard anyway.
I use DesktopGL for MacOS, Linux and Windows and have to do pretty much nothing to get the builds to work on the respective platforms. Packaging the macOS app is a bit of a faff but once you have written a script to do it it’s easy. I even build the Linux version on MacOS which I never thought would work but it does!
I have a separate project for the Windows build but that’s only because I couldn’t figure out how to import different native APIs per platform for the Steamworks stuff. If I wasn’t using native libs I could run them all from the same project no problem.
One issue I ran into with 3.6 DesktopGL is that is does not play nice with OBS and other streaming software. Screen goes black and/or freezes in the recording. This is/was a bit of a bummer. I don’t know if this is any better with 3.8 as I haven’t specifically tested it. I considered switching to DirectX for the Windows build because of this but decided against it when I read about the superior controller support in the GL version (if this is true)!!