Profile vs T-value vs Colormap

I think we are missing some points here. for your profile report can you include max and min and find those points? 

Since you do not datum to anything, I can only presume some of your output methods do not consider any bestfit practices which may be applied to other calculations. 

--This is difficult to answer without seeing the code and drawing requirement.  Is the profile control unilateral? Bilateral? unequally disposed?  You say 0.5max, so that's ±0.25mm from the true form of the cad model, (bilateral, correct?).  Is it controlling the entire cup as one dimension? 

Either way your profile output is definitely not adding up to your Tvalues or heatmap deltas, and methinks it's related to bestfit or lack thereof.

My understanding is that form only profile would be +.50/-0, form and location would be ±.25

All points are here, and graphical analysis looks like this :

External points looks all OOT.

Here is the callout, so it's bilateral, and i'm pretty sure the engineer just want the big radius to be well shaped:

well there ya go. you have some red in there

In my opinion, that callout is ambiguous.  If it were me, I would ether bug controlling design authority for clarification, or just move forward with interpreting it at face value: exclusively interpret it to apply to the radius, which is continuous, to become a donut.  This is inherently controlled "all around", BUT clearly defined as a bilateral zone, ±0.25mm from the radius nominal.

So if it were me, I would do the following:
1: remove analysis of the base plane inside the cup.
2: prudently exclude blend radii at top of cup.
3: measure it as individual radii, then construct a scan set of all the radii combined, bestfit align to the combined radii set, then produce one profile of a surface to that set.

that sounds exhausting. I don't think he's wrong scanning the entire surface as hs has it set up now. i'd def increase the scan density so I can see what's going on though

less exhausting than over-inspecting and rejection of potentially acceptable goods?

but why measure as individual radii? 

why not measure the flat/plane, level and origin, inspect profile/radii as shown with scans, and report the profile? what does best fitting to the radii do?

Paste with pattern FTW! 
If there are datums on the part perhaps be aligned to them, I get trying to best fit to the radius itself but that is rarely what the enginerds intend when they call it out like that. They would typically say they want it comparted to the nominal model location, which when you machine the part the datums establish the nominal model location in reality. Checking it to a datum will also allow you to give the machinist meaningful feedback about their part thus allowing them to make corrections. 

Definitely steer WAY clear of the start/stop of the radius for your pickups though, that will throw things off.