he basically ignores the concept of sub-component overlap potential

I think you may be misreading Yee's paper - his procedure tries to find orthogonal (uncorrelated, r ≈ 0) motivations. Non-overlap would imply anti-correlation (r ≈ -1), which is something different. In fact Yee criticizes Bartle's Taxonomy of "Player Types" for using phrasing that implies anti-correlation. From the paper:

Bartle assumed that preference for one type of play suppressed (e.g., Achievement) other types of play (e.g., Socializing or Exploring). Also, it has never been empirically shown that the four Player Types are indeed independent Types. In other words, several of the Types may correlate to a high degree.

The factor analysis revealed that play motivations in MMORPGs do not suppress each other as Bartle suggested. Just because a player scores high on the Achievement component doesn’t mean they can’t also score high on the Social component. This is supported by the data - correlations among the 3 main components are weak (r’s < .10).

Note that the implication of grouping the sub-components together in the "second PCA" is that they tend to be held (or be absent) together. So I believe your example is actually captured correctly by Yee (though the paper buries it in dense statistics-ese).

The idea is that the sub-components still describe differences between, say, Achievers as much as possible, even though the sub-components certainly don't separate players into 180-degree polar camps.

For this illustration, the distinction is a bit trivial regardless - ex. if Niantic focuses only upon one motivation, they are still ignoring other motives for play. The difference between saying whether some aspect of a game "satisfies some players" or if it "satisfies some of the motives of some players" doesn't really change the criticism from a design standpoint - it still satisfies players only partly. :p

Achievement -> Mechanics is always difficult in such a long-term game as well because many prefer to customize to their own strengths or interest areas. Niantic may want to either go a different direction or intentionally hide data from players for meaningful reasons.

While I agree it would be difficult, things have spiraled out of control. I would even say there's a culture of ignoring Niantic's wishes and scraping the hell out of game data.

Now that I think about it, it is possible to appease the desire for mastery by channeling effort into different things: off the top of my head, things like offering instant-feedback mechanisms for how well you are playing (damage per burster, deploy distance, etc.). It's possible the "minigames" (charged bursters, glyph hacking) are an attempt at this, but it's a bit of a roundabout way of tackling it, and I'm not sure it's enough.

even though I again feel Yee's classification to be a bit lacking. "Having an interest in customizing the appearance of their character." Would, for instance, people who have the timer overlay for the app count as customizing their "character," even if no one else is viewing it?

I believe the original context is graphical MMORPGS ("EverQuest, Dark Age of Camelot, Ultima Online, and Star Wars Galaxies"). Scroll down to Appendix 2 for the exact survey questions.