If taking it seriously as a game to make and sell, I imagine it would split three ways.
Breeder mode, where you run a mill and balance time and difficulty vs rewards, meaning you need a system where profit means something by perpetuating a loop of upgrading facilities and tools so you can do more, to afford more things that let you do more, with achievements and nontool rewards to mitigate the “why am I doing this again?” feel. Stardew Valley comes to mind, except you have to work against factors like how easy they die or kill each other, and how stress reduces their profitability so you need to find that sweet spot of acceptable cruelty: an ectogenic tank would be insanely expensive but gets you straight to birth and you only need egg/sperm donors which can literally consist of surgically removed ovaries and testes, so welfare means ansolutely nothing and you can literally sell them straight out of the tank as adults which puts 100% of the rearing on them, like a super premium Foal-In-A-Can. Or letting them loose in a field designed to weed out the weak and stupid, making a breed of better ones that can survive extensive Abuse or just be less terrible pets. Mass production vs quality product, with upgrades letting you pursue your choice easier. Concern, or possibly perk, of Ferals bringing random bloodline traits or kidnapping some in outdoor enclosures. Sell them pretty with all personalities for a slot machine effect on profit with eugenics to press your finger on the scale, or take effort to make ones who are amiable or interesting ones which has a delay on profit and can boost undesirable ones.
For the Hugbox route, just having the “hard mode” of just caring for them. Hell, maybe intentionally keeping some Hellgremlins and keeping them satisfied, or allowing in Ferals to Abuse them/be Abused by them.
Finally, raw Abuse. Plenty of ways to torment. Systems of causing different kinds of targeted damage, and how they attempt to continue to survive. You could poke out an eye, remove legs, and still profit. Designate one for Abuse by others by weakening their ankles, but leave their teeth. Keep the worthless ones as pets, let them loose in the wild and change the Feral population traits, or leave fences made from rotting bodies all around the enclosure.
When generating them have “never evil” and “always evil” as rare traits you can breed into a bloodline, then for the rest use it as a percentage chance on behavior with a starting point based on genes and pushing towards increasing or lowering it based on their life experiences, a second meter indicating violence vs brattiness.
I’d ignore concepts like tax/human expenses, saying you have investments to cover your needs and all your luxuries need to stem from the Fluffies which cost money to care for. To enable Hugbox or “just my pets” routes there would be an element of foraging or gardening. In the latter you could upgrade it to protect from Ferals, even be automated. Or a cheap machine that spits out nutritious slime they hate and produces lower quality ones so you can disregard the system entirely once you start to profit. While foraging they are more likely to hurt themselves at home, but you can encounter Ferals which prevents a loop of them dying and you having no money to get more.
Maybe let you choose who to sell to. Abuse needs bulk but has particular requests, stores want unique coats but standardized bodies, the general market may not sell but unique things may go for a lot, food requires other properties like cleanliness and fat+muscle tone, and so on. A restaraunt may suddenly pay a lot for three Foals of a particular type, an Abuser may suddenly request an innocent sterile female or putting a brown worthless Fluffy up for market may get a sudden huge purchase from a rich kid who saw it looked like a video game character you had no knowledge of. Maybe one has heterochromia, another week yellow is worthless due to a random terrorist event in Canada being associated.
Again, Stardew as a model. Achievements are general, you can choose how to pursue them and the game gives workarounds if you dislike something. There’s plenty of distractions.
