The truth is that, as you discovered, there is no data provided that canonically defines the creatures you can select as a familiar. Likely by design, the familiar is currently an undifferentiated bundle of stats relying on the player to flavor. This may change with the Gamemastery guide or Bestiary 2, but I wouldn't count on it. In other words, a familiar follows the template described in the familiars section regardless of what they are - they have your saves and AC, 5 * your level hit points, size tiny, low-light vision, and either a land speed or swim speed of 25 feet. Beyond that, they are an animal (further limited to tiny sized animals) unless otherwise noted by the feature that gives you the familiar (such as the Druid's leshy). That's the base, as you've noted, and the actual animal you choose is little more than set dressing.
I feel that the obvious intention of the designers was to not have one familiar be inherently better than another - "oh, I'll take the bat because it has blindsight and flight" or "I'll take the spider monkey because it has hands", and so on. So all familiars start off on this level playing field, and if you want your familiar to have flight or blindsight (not currently available) or opposable thumbs, you have to buy it using the familiar abilities. To this end, what the rule you are asking about is stating is that if you do happen to choose an animal that you (or a reasonable person) would expect to have one of these abilities, you have to take it, reducing the number of other abilities you can grant. Which, in a way, makes some animals inferior to others because you now have more limited options each day when selecting your familiar and master abilities. So, yeah, the implementation fails to support the intention, assuming my supposition is correct.
Realistically (with GM approval, of course), you could argue that your owl has a broken wing (or some Finding Nemo birth defect) that prohibits it from flying normally, so that if you don't want to spend a familiar ability on it one day to allow it to fly, it simply can't, and you aren't penalized for selecting a flying creature as a familiar (since the familiar abilities, as the artwork in the book calls out, allows you to put wings on a cat if you choose, so any familiar can fly).
In short, taking a familiar that naturally has any of the familiar abilities is a penalty by the rules as you are now locked in to spending those points, where it is optional for a normally less gifted animal, hence why I propose the hobbling of a creature's natural abilities as above so that you can have your owl for cosmetic reasons, but not be limited in your ability selection for it.
More to your question, you are correct that there are no stats for an owl. There are stats for a viper and an eagle (though it is small), but other than those, the closest that you can get to animal stats would be the animals described in the Animal Companion section, but they are size small (or med/large in the case of the horse) and are supposed to be considerably above average examples of their species, so it provides little more than an extreme upper bound. Here (and in the stat block for Eagle) a bird has a fly speed of 60', which you can't even get on a familiar if you get both Flier and Fast Movement (40' fly speed). So, it's far from perfect, and "bird" covers a lot of ground - it'd be fair to argue that owls have darkvision while hawks don't, and neither of them has blindsight, while bats should.
The best advice I can offer, aside from diving into some Pathfinder 1e books or waiting for more 2e books (or official online resources) to come out to clarify, is to just go with what makes sense and work it out wit your GM. Cats, owls, hawks, snakes (ignoring poison), and so on are pretty easy, but a bat, since there is not blindsight familiar ability, is a different beast (pun intended) entirely. Some would argue that blindsight might be too powerful for a familiar ability, others would say just house rule it in to the list, and others might suggest disallowing bats until official guidance is available.
Bottom line, it's a GM call, but I wouldn't sweat it since you have to pay for the feature anyway. It actually works out in the player's favor to say that owls don't have darkvision (or fly) and cats don't climb, so you can choose those abilities if you want, but aren't forced to.
An additional thought
The rules on familiars say that familiars can attack using your level as the modifier, but the lack of stats means we are on our own as far as determining the amount and type of damage.