In truth, I just wanted an excuse to have short-haired fluffies with the fleshy muzzles and then I thought “fuck it, I’ll come up an excuse for there to be both types running around”.
You can think of Gen 1s as pre-breakout fluffies, in terms of their breeding.
Cheeky jokes in the above post aside, there are no real observable differences in Gen 1 and Gen 2 behaviors, It’s mostly aesthetic.
Neat, I’ve always preferred the flesh-toned muzzles myself, but this is definitely a good way to allow for both
Variety is the sweet spice of life, and all that. Sometimes Papa Poopiest just wants to have his cake and eat it too. 
I also felt like this made perfect sense, that fluffies would already start showing some slight changes based on natural selection in the wild and breeder preferences. Considering a single fluffy generation can, at the very least, come about every 4-5 months, (although you’d be pushing it). So I imagine a lot of mating preferences have become established since the breakout.
The issue with the theory that ‘wild breeding causes evolution’ in fluffies, is that real animals that have escaped, crossbreed with compatible wild animals, causing hybridisation.
With fluffies, that’s not possible as there are no wild compatible animals (unless you have them crossbreeding with wild pigs or something), so any escapees that breed would be breeding with other escapees, and specific traits of that bottlenecked group would become the norm across the whole population.
Actually that’s an interesting story idea - fluffies are genetically compatible with certain wild animals and feral fluffies end up hybridising with them, resulting in more durable fluffies, but less of their inbuilt genetic programming.
Eventually this comes to a point where there are hybridised herds, with only some fluffies retaining the ability to speak, while others have lost all Hasbio programming and behave pretty much like wild animals.
Family dynamics would be interesting with otherwise normal fluffies taking care of their mute siblings or parents.
My line of thinking was more that “pretty” looking mutations would become the preference.
If you took a standard G1 mare and made her choose between a fluffy with softer fluff or cute freckles, versus a standard fluffy with no unique traits, a fluffy will more often than not choose a prettier mate. It’s just preference. Also I imagine that mutations tend to pop up quite commonly amongst fluffies, being that they are synthetic life forms and their DNA is already horribly hodgepodged together. And when I say mutations, I don’t just mean the cute and quirky kind, I imagine that cancers and degenerative conditions are prevalent as well.
I absolutely love stuff like this, seeing how people will apply things like genetics to their fluffy universe. It’s fun to see how other people’s worlds work.
The idea of multiple versions of fluffies that evolved to adapt is such an interesting concept.
I agree with your headcannon; IRL we have dogs as an example. Their massive variety in races comes from artificial breeding. There’s no reason to think that we wouldn’t do the same to a biotoy designed to look pretty, if we did it to actual animals.
