I think CT has indirectly addressed your question through various livespills, training lab, and forum posts. In short, pullup training can certainly be incorporated into the program. For example, CT has his mma client do multiple sets of submaximal chins throughout the day, everyday. Obviously your capacity to recover from this will determine how much volume and how close to failure you get. General rule of thumb being as many as possible without affecting your performance in the HP mass workouts the next day. This should address question #1.
As an aside, it seems that CT feels that for optimal back development, the "hold and squeeze" is crucial; if you can't perform these sufficiently with chins then, at least from the perspecive of lat development, they may not be the ideal main movement in your lat foundation day workout.
Regarding replacing traps/rhomboids/mid back work with pullups, CT has specifically delineated between lat work and "supporting back musculature" work. The latter should be worked in tandem with your upper body pressing muscles to promote shoulder health, etc. Chins/lat work in general is done on the "foundation day' which is SEPARATE from the upper back/shoulder supporting musculature work. So I think he advices not to replace traps/rhomboid/mid back training with lat work and vice versa as they serve different and important functions. This should address #2.
Regarding question #3 about negative chins, I think CT would ask what your primary emphasis would be. Obviously, negative chins have been used with much success to increase pullups (particularly for those who couldn't do many bodyweight pullups to begin with). The HP mass performance is not a pullup specialization program and such principles as eccentricless training to minimize CNS fatigue are outlined by CT as a way of increasing volume/stimulation without exceeding one's capacity to recover...to serve the purpose of BULIDING muscle. I imagine if your primary goal is to just improve pullup performance, then doing submaximal repwork daily or several times a week as outlined above would be an ok "addition" to the program. Most pull up specialization programs I've seen focus on submaximal work daily or seveal times a day (e.g. as outlined above) rather than heavy eccentric emphasis. You could probably do negatives on your lat/bi foundation day if you really wanted to.
Since I also love pullups I'll share what I've been doing. I can do about 35 chins strict form before failure so I like to do sets of 10-15 pullups throughout my workout with a fast, somewhat loose form and certainly no emphasis on the eccentric. I treat these as additional volume and fun; they dont really affect my performance. I usually stagger them in between my upper body pressing and my supporting musculature work. Throughout the rest of the day, I bang out several sets of pullups at home, never to failure.
Hope this helps and someone feel free to clarify if I missed something.