I think a huge reason so many brachycephalic breeds have issues breathing is entirely based on their weight. My sister has a Pug named Zoe who was horribly overweight when they bought her- and had the typical Pug breathing problems. When she took the weight off of Zoe, she was incredibly athletic and energetic- and the breathing problems were completely gone. I think the reason show dogs are so targeted for breathing issues is because they are kept so overweight in the ring (this is true for all breeds, not just brachy breeds).
The combination of no muzzle and obesity certainly is a bad one. Still, that doesn't mean that not having muzzle isn't in itself an issue (just like being obese is in itself an issue). Those extreme brachy traits can cause dental issues, breathing issues, eye issues and other problems. I know several Pugs (BYB FWIW) who can't hold their tongues in their mouths. Their tongue just constantly sticks out and is dry. You can hear every single breath those dogs take too. I know multiple one eyed Shih Tzus and Pekes who had eye injuries due to their eyes too easily popping out their heads. And various Brachy breeds who have constant eye issues. So it's not
just a matter of muzzle length. And it is not just show breeders who's dog have these issues. I have seen some really extreme BYB/petstore bought examples too.
As for the comment that all breeds are kept overweight for the ring...I'm involved with showing two breeds and neither is shown fat. If anything, you're likely to see dogs in the ring who could stand to put on a couple lbs. Actually Whim lost to Cherry at our UKC National because she was about 4 - 5lbs overweight (per me) and Cherry was more fit. And when Savvy got a bit chubby as a puppy, his breeder was quick to tell me he was eating too well
I know a long, long time Boxer breeder/judge who definitely expects Boxers to be shown well muscled and not fat or soft.
So it is fashionable in some breeds to show fat dogs but that is not the case in all breeds.
I don't think it's unrealistic or wrong to want a dog who is a less extreme version of the modern trends. If I got another Collie, I'd want a dog like these:
There is nothing about them that doesn't make them Collies. I would even argue they have nice breed type but are just not "ultra-typed", they don't have some of the extreme features you see more typically in the modern version of the breed. That is what I like in the breed, regardless of what people consider "correct" right now.
Also I strongly prefer Corgis who have some length of leg and are a bit shorter bodied. That doesn't mean I don't like Corgis, it is a variation in type found within the breed...it's just not what breeder in modern times consider "typey". If we were to get another Corgi though, you can bet I'd be looking for one built like Ziggy or Emily's Keeva.
And GSDs, I also prefer the more moderately built dogs regardless of lines. Luckily in GSDs there seems to be more acceptance to seek out whatever floats your boat. Although I have been told by people that anyone not breeding AKC show quality GSDs was a BYB (people who said the reason they didn't get a GSD was because of the way show GSDs are built).