Yes it was on purpose, for a couple of reasons.
First I tried to avoid virtues that vary from character to character. There is no one Magical Focus virtue just an infinite number of virtues that fall under the magical focus umbrella. The same is true for Side Effect, Special Circumstances, or Mythic Blood. I also tried to avoid virtues that seemed to make Magi better at doing things that all Magi can already do. Like your various puissant and affinities to art. To me these have the same relation to the Arts and hermetic magic as an affinity to single weapon has to do with fencing.
The Virtues I did judge to be "Incorporable" instead allow the holders to do something different that no other magi can do and seam to rely on some sort of methodology lacking in general hermetic theory. Two borderline cases illustrate my philosophy.
Secondary Insight made the cut just barely. It improves study something all magi can do. But it does it in a unique way not matched by any General learning virtues. It is also described clearly as a method in it's splat.
Flawless Magic didn't make it on my list. To me the majority of it's benefit seemed similar to other learning virtues. I've usually viewed Flawless Magic an affinity for a broad range of closely related skills. With a little bit of independent study thrown in.