Now that I have finished customizing my crosstrail comp, I find it both very comfortable and impressively agile.
I confess that the changes were mostly designed to increase comfort, but the handling has also considerably improved. I think.....
By that I mean, I'm not sure how much was inherent to the stock bike, or how much is a result of the mods.
The most significant changes were done shortly after purchase so comparison is difficult.
They were.........swapping out the stock road/trail tires for Schwalbe marathon supremes, which is a road touring tire.
I also changed the stem to raise the handle bar from about even with the seat to a little above.
Other changes that I made might seem to be contrary to popular wisdom regarding agile handling, they were
swapping the thinner narrower specialized targa saddle for a selle smp trekking model, and replacing the seatpost with a Thudbuster ST.
The other changes I made that I think improved agility was swapping out the stock nylon platform pedals for raceface pedals with pins. very sticky.
I also replaced the stock grips with ergon GP4's with have bar ends,
The crosstrail comp comes with specialized's M4 frame which is a stiffer aluminum than the usual A1 frame.
The stiffer frame should add to agility as well.
Anyway.... because of my neck arthritis I have to be careful about being jolted by potholes etc. so I experimented with locking and unlocking the fork.
I found no difference in handling at all between the fork being locked or not. I now ride with the fork unlocked at all times to protect my neck from injury.
the bike handles beautifully. I love how quickly I can avoid hazards, cut corners, stay on my chosen line etc.
Is it the geometry of the bike, the stiffer frame, or the mods that made my bike such an agile handling for a full blown hybrid?
Interested to hear your thoughts?

Probably a combination of perfecting your position and getting better at riding. Practice does make perfect

It could be you have become a better rider.

Get a rigid fork and wider tires and don't worry about potholes.... the tires and frame should absorb them before it gets to your back and neck.

I wish.
Problem is the reason I ride a full suspension hybrid is because it doesn't take much of a bump to cause severe pain. I really wanted a Sirrus carbon but when I rode one, I deliberately hit a crack in the pavement.
BAM! I had severe pain for almost a week. No, there is no question but that I need a front suspension.

I believe both of these assumptions to be true.
I have never been as comfortable and secure in the 11 years since returning to cycling as I am on this bike. I really nailed it when it came to buying the correct bike and modifying to compensate for my physical shortcomings. I truly believe that having a well fit bike with as you so eloquently put it "perfecting my position" gave me the confidence to reach farther.
But i was actually wondering if the stiffer frame adds to agility and handling ability or is there some other reason why Specialized might have put this frame on the higher end crosstrails?

Bicycle handling is most affected by the geometry. Factors such as wheelbase, head angle, rake, and bottom bracket height affect "agility" or "stability" on a bicycle more than frame stiffness differences between two tiers of Al frames

Agility? It's the tires that improved that. What size did you replace, with what size.

I found an amazing change when I switched my Crosstrail to Supremes, and even more so when I put a 35 on the front! I retained a 40 Supreme on the back for comfort, and let the front shock do the job on the front. The best of both worlds!

Changing both tires to a different size will alter the BB height. Putting a smaller tire up front will steepen the head angle a bit and lower the bottom bracket a bit, all geometry changes that affect handling

I replaced the specialized trigger 38's with Schwalbe marathon supremes 35's. I did not notice any reduction in comfort but was immediately impressed by how sticky they are in the curves. Really fun. Now that you mention it, I'm sure these added considerably to the agility. Turning on a dime for example.