Ink Manager does not give you any output values—it shows expected ink densities which are not separation halftone values.
You have to open Output Preview where the Separations panel gives you the output CMYK values under your cursor for the chosen destination profile (Simulation Profile):

You can also use Preview>Object Inspector to get an object's assigned color profile and native color values.

Yes Output Preview is the one to inspect, you are right.
Because the original problem keeps digressing into other topics through this post, and having since corrected my problem by using the PDF/X1-a preset solved the issue I'm going to close this question.
Thank you for all your help.