As I'm sure you know by now, choosing a pet gives you a couple of points of starting skills. These points are applied before you reach the first study screen (after all, you've had your pet for a while) but the text that explains why those skills go with that pet doesn't happen until later, because it didn't fit the narrative flow to be at the start, and there's no popup indicating the effect of the pet choice when it happens.

Was this confusing to you? No solution is perfect IMO. Possibilities:

• Leave it like it is - people will figure it out
• Make a skill gain popup when you select your pet type, even though this may be distracting
• Don't gain pet-related skills until the explanation before the Social Phase and have a popup then

I think it works as it is, because few people are going to want to select their pet with stats in mind until a re-run. If there is to be any change, it might be from mentioning the pet skill gain the first time the skills screen is reached, during the explanation of the skills. It's the first time the player will need to take the pet skills information into account. A first-time player is unlikely to reset simply because the skills were not as expected (especially since experienced players can check the skills on selecting the pet if they're looking for that information).

I think it's fine as it is. Chosing your pet and seeing the stats you start with from the get go is helpful. 

Maybe hints on the pet selection buttons, like there are hints about what skills might be tested for some choices? So Golden Viper gets a hint for Allure + Contortion, the Ebon Blot gets a hint for Big Guns + Hiding, the Mechanical Hawk gets a hint for Hunting + Repair?

So I've done a couple of runs, and this is the first I've learned of the pets providing skills -- the only thing I knew of was the mood reset when you visit them during Social phases. So, yes, giving some kind of information about it pop up would be great. XD I'm not much fussed on when, as long as it's explicitly said at some point.