Sometimes there is depending on whats a stock shaft vs. an upgrade.

Cool Clubs can/will use shafts not in the Titleist matrix. That's one big variable. Not saying that is good or bad, just different.

Personally if you're going to pay Cool Clubs for a fitting I would just sign up for a Titleist Thursday event as they are free and with a certified Titleist Fitter. If there isn't a Titleist Thursday event close enough for you then maybe pay for the fitting at Cool Clubs. Not sure how well Cool Clubs would produce the clubs for you but it can't be bad if they offer fittings and club making for Titleist?

I believe it will depend on if you pure the shafts, hard or soft step them, etc

I think Titleist has always had the highest quality/consistency in building to specs, but I've heard they really have been focusing heavily on that lately. I think either way, you'd get exactly the specs you ordered. I believe if you get your clubs built by Cool Clubs, then they do free adjustments whenever needed. But if you already know all the exact specs you need, I wouldn't hesitate to order them from Titleist that way.

You should have no issues with anything custom built by Titleist. I just toured the plant where all the custom work gets done and they have the proper QA in place to create a quality set of custom clubs.