When Corgis and Dachshunds were first bred they were bred for a purpose. Supposedly in the case of Corgis to herd animals by nipping at heels, and because they were small the resultant kick from the cattle would go over their heads???
The Dachshund was a small prey hunting dog so they could flush animals out of underground warrens, lairs and setts.
I would assume that such dogs were fairly disposable so when working dogs got health issues from their dwarfism, they would be replaced by younger fitter ones.
Nowadays we want dogs and cats to be healthy and happy for as long as they can be, as most are beloved members of families.
The furore around breeding achondroplastic cats is that how do you prevent a cat with a normal feline brain from jumping on sofas, or jumping down from trees or all the other things that put huge strain on its back and legs. Achondroplasia doesn't only mean short legs, there are other issues that come with achondroplasia.
Cats and dogs are extremely good at hiding pain, they often only show their distress when they are in agony or the pain is intolerable, so healthy and "happy" is perhaps not the case.
So just because the Munchkin acts like a normal cat doesn't mean it is not suffering to do so.
In this day and age in a civilised society, we strive to reduce suffering to the minimum for ourselves and our extended pet family. To deliberately breed animals that have a high chance of suffering merely for cosmetic effect cannot be condoned.
The GCCF will not register such animals as they are the result of a "harmful genetic mutation".
http://gccfcats.org/pdf/BreedingPolicy.pdf