A flying monster is pretty common at any level. There's LOTS of stuff that can fly. Or heck, even climb well. I doubt there's a single CR from 1-20 that doesn't have at least one critter that can fly.
Though you would be hard pressed to find detailed rules that say you somehow "must" use flying foes as they are "common".
Then of course there is the adventure focus problem. Sure "monster X" is "very rare" all over the world. Sure you can walk through whole kingdoms and never see a "monster X". Oh, but head over to the Cursed Ruins of Azal-Zah, and guess what "monster x" becomes common.
OTOH, creating an anti-magic zone is a pretty obvious DM thing. It's the DM very clearly giving the casters a giant middle finger.
But the DM doing lots and lots of things directly against the mundane character is not "giving a finger", right?
Anti-magic is, honestly, super rare. That's an 8th level spell. Not really something your 5th level party should be bumping into every day.
I'm fairly sure I have never seen this "rule". Yet many DMs do it.
And again, "anti magic" is rare in the Farmlands of Gorll......but how "rare" is it in the Magical Tower of Zorn the Mad?
Plus the Antimagic Field spell negates ones own magic.
I know in my quick example I only mentioned anti magic. So to be more clear I'm also talking about: Dead magic, wild magic, suppressed magic, absorbed magic, and lots and lots of other types of effects that effect magic.
My bigger point is how nearly ALL DMs have NO problem telling the player of a mundane character "sorry your character is useless, go sit in the corner" ALL the time.
BUT
Those same DMs would NEVER EVER even DREAM of saying something like that to a player of a spellcasting character even for a couple minutes.
Example Two:
Player of mundane character: "Ok, I get out my axe and will chop through the wooden door...."
DM- "Oh your axe just bounces off the door and you can't cut into it at all!"
Player of mundane character: "Ok, I get out my tools and will take the door off it's hinges..."
DM-"Oh..um...no...you CAN'T the door is too well made! It's impossible!"
VS
Player of spellcaster: "Ok I will use Magic Hand to touch the door..."
Dm: "At the touch of your MAGIC spell the door swings OPEN!"