I believe its an option when you right click the game in steam.
If you don't want the desktop icons, you don't need to relax the flatpak permissions for the xdg-desktop. Just the first two for allowing steam to see the icons and the applications folders.
If the right click option isn't there in steam, there might be a way to regenerate the icon, but off the top of my head I'm not sure. Reinstalling the game should do it but that's a pain for larger games.
I'm on the fence about this since how would proton verify that "best practices" were followed? They are a privacy focused product and a feature like that could be used to decrease their services privacy. This author would likely implement best practices and many other likely would too, but say a competitor wanted to prove that their product was more secure, a feature like that could enable a competitor to showcase a security "flaw". And since headlines are all people read these days it would be damaging.
The feature the author described would be great but ProtonMail would need to make it fool-proof and temper-proof which requires a lot of Dev time and effort. I'm still waiting on proton bridge to work with calendar and contacts. Or contacts birthdays to show up in my calendar.
Like I said, its a good feature, but its likely a large ask for a niche group of customers.
No worries. Yeah I ran into this same issue with flatpak steam and got it mostly working about a year ago and then distro hopped. Lost the changes for some reason and just didn't bother fixing it lol. Glad you got it working!!