W shapes are rolled with a consistent inside dimensions between the flanges (maybe a couple inside dims per nominal depth), not a depth, so you'd expect a W14 with 6.5" inches to be somewhere around 20-22" deep
Using a dummy elevation for TOC is pretty common I would think. Using 0 is pretty bad practice because you have negatives on the drawings now, but it's best not to put an elevation on the drawings until you have a known survey.
The only reference is the code itself and an understanding of what the one way shear equation represents. The code kicks you out of one way shear equations in D regions, and these equations assume a diagonal shear crack with some frictional force along the crack. In a D region there isn't space...
Is there any actual test data to show S+T is unconservative for pile caps? Of course if you just punch the formulas in ACI 318 now that they have properly accounted for size effects in deep members, a one way failure mode is going to control, but that's not a strictly correct failure mechanism...
This is what I see being needed to truly sign off on the building:
-A day or two with a tape as builting it
-A certified weld inspector to visually inspect the welds
-A couple coupons taken to determine steel strength
-A few weeks of analysis
-Probably more lateral bracing installed since these...
There are span tables for checker plate in the AISC manual as well - for deflection, an L/xxx isn't already the most approriate. As long as the deflection is under 1/4" people are generally comfortable
That new brown foundation is a monster. Suspect the actual potential for settlement is minimal. If you have clean granular below, the elastic settlement will all occur once you pour the behemoth, so I wouldn't bat an eye over bridging the two with the pump foundation, maybe dowelling the slabs...
Thicker plates would resolve it, you're probably limited by the supporting flange now. So a flange doubler and stiffeners is your next bet, if you can't upsize columns
If the columns settle or deflect they will stress the crane beam. True of any continuous beams, but in most cases we aren't running over them repeatedly with heavy suspended loads.
Singly or doubly symmetric sections would not have a skew angle so no Lz check. I read it the same as you but can't say I've dived too deep into the OWSJ space. I suspect this is a new addition to the code (well, since 2014 which is my hard copy) that hasn't percolated through the manufacturers yet.