The answer is yes.
After all, most dogs are brachycephalic when compared to the wolf and other wild dogs. Short muzzles are a diagnostic of a domestic dog.
However, when we breed for healthy conformation, brachycephalic dog breeds are going to have to have some muzzle– enough for the all the teeth, tongue, and soft palate. One of the reasons why these dogs have so much trouble breathing and cooling themselves is they don’t have enough room for their tongues and soft-palate. The tissue in the soft palate winds up obscuring the trachea, and that prevents air from flowing. In a dog, that also prevents the animal from effectively cooling itself.
So when we evnetually get around to correcting breed standards, we are still going to have bulldogs, pekes, bostons, and Frenchies. It’s just that they are going to have a bit more muzzle.
And I don’t think that’s too much to ask.