I like the guidelines. Honestly, I wouldn’t mind a few more. Other app stores have WAY more requirements for art assets and metadata.
The first time I made a mobile app (many years ago when I was basically an amateur), I was like, “What the hell? I have to make all these icon sizes?” But it was good for me to be forced to comply with professional standards. I don’t think Flathub should go the Apple route and require everything be just so but, as annoying as it may be at the time, it’s good practice and it’s good for the wider Linux desktop ecosystem.
Favoring modern design on the icons is good. It doesn't state that it has to be flat, it just says that it should at least follow some modern design guidelines so that the app doesn't send the impression of being an older, unmaintained thing.
If I find an app in Flathub that has an icon that looks like it was made 20 years ago I'm shocked when it ends up using modern frameworks. I think Inkscape and GIMP are the only examples that comes to mind.
People erroneously conflate modern and flat. Flat is used as a bogeyman.
Plenty of old icons are flat, and modern icons are moving away from flatness. The GNOME-y icon they showcase is clearly 3D, and multiple flat ones they show they state they disapprove of - 3/4 of these are flat and disapproved of.
Saying "ideally, app icons should give the impression that the app is actively maintained, not an abandoned mid-2000s project" doesn't mean "make it flat or else"
Some of the icons they say are good aren't flat though, they feature 3D shading and clearly show depth.
Take that GNOME-y looking one for example. It looks modern, but the workbench, screwdriver, spanner, and hammer all have shading and depth. They are 3D objects. The genie-lamp icon looks far flatter, and that was disapproved of.
Flat and modern aren't really the same thing. There are old flat designs, and plenty of modern icon designs are slowly becoming more 3D again.