Cats are the exception, not the rule as far as that goes. As far as I can tell, it's the only time that qualities are mentioned on a sheet?
Again, you seem to be forgetting the sentence before that, which puts the whole thing in context.
To me that pretty clearly changes the meaning of your quote. First, a guide is just that, a guide, not a requirement. Second, when added, the bolded section comes across as a warning that natural qualities do things like add to characteristics that should be taken into account when using said guide, as it will throw off character creation.
Nor does it say that you get them.
The only real requisite is for them to have an essential virtue, a thing that pretty much every example ignores (the irony isn't lost on me). But yes, yes he is.
Ultimately this means it's up to @Arthur to adjudicate in the case of Animals of Virtue, but as you say, they're a special case.
Pretty sure this is the sort of thing that @Vortigern was talking about in regards to tone mate. But to your point, it's quite easy to do. Just look at his virtues/flaws and abilities and you get a pretty solid idea (more or less). That said, ultimately it's impossible to separate Skepsi from his magical side entirely, as that's just not how characters are built in Ars. This isn't nWoD or something where we're stacking templates on top of one another.
I won't disagree that Ars is often a mess of unclear rules and conflicting examples mate! But to your point about the eagle, that's not necessarily true. An eagle made of wind very well might not have the sight afforded to his mundane counterpart, but an eagle of virtue would likely have a personal power that would give it sight on a magnitude that its mundane counterpart could never dream of.
Uh, I posted the basics of a sheet almost four weeks ago now and literally asked for feedback? In this exact thread.
The irony here is that giving Skepsi and other familiars natural qualities actually boosts the power level, not reduces it, so your argument just doesn't make a lick of sense to me?
I think we've got a few folks who aren't particularly active on the weekend, so I guess we'll see on Monday!