The Clarkson is a great floor plan, but with that large size you could do a lot.
I don't think it needs extra rooms as I prefer spacious rooms over more smaller rooms which divides the space up more but that really depends on your lifestyle and living situation. Dens are overrated unless you work from home full time. There is room on the other side of the 2nd bathroom wall to the left to put a nicely sized desk, either freestanding or built-in.
The 11' ceilings is only on the PH level, where the same floor plan on other levels are 9' with select floors having 10' ceilings. The PH level is obviously preferred because not only of it's exclusivity, but it has only 7 units on that floor, has better views as it will clear the ugly office building across the street, and as mentioned previously the taller ceilings.
Extending the counter outwards a foot in the peninsula for a breakfast bar is definitely a must as you can effectively use stools there for informal dining/seating. And I agree that extending the counter 2 or 3 feet to the right would provide needed counter space for food serving or prep, or even more casual dining or entertainment space because you could add a few more counter stools around it.
The enclosed toilet in the master bath is a good idea if you are living with a spouse, trust me! I would rather have it frosted glass enclosed (or frosted up to 6 or 7 feet tall) rather than drywall so that it feels brighter and less claustrophobic.
I would rather have a walk in shower instead of a tub in the second bathroom as guests will shower more than take a bath and it will make that bathroom appear more open and spacious.
I would add a door for the walk-in closet for the 2nd bathroom while for the Master Bedroom closet I would have a custom California Closet installed as it would still look attractive when still exposed -- though doors in the closet system could be added to conceal more of your closet if you really think seeing your clothing collection is too cluttered and overwhelming.