Q: For the first example, the color zones were just added using the axis settings?
A: Yes. You can add spec limits to your response variables (https://www.jmp.com/support/help/en/16.1/#page/jmp/spec-limits-column-property.shtml) and have them appear on your profiler plot, but you would need to edit the axis settings (https://www.jmp.com/support/help/en/16.1/#page/jmp/customize-axes-and-axis-labels-in-graphs.shtml#ww781878) to show a colored spec range.
Q: What are the capabilities of JMP to design clinical trials? I see that JMP can analyze data from clinical trials, but I am not sure if we can design them.
A: JMP currently is not used much for design of clinical trials. However, there is no reason why it could not be used. Clinical trials are different from industrial R&D experiments. In some respects, they are simpler because there is often only one factor: drug or placebo. The more complex aspects of clinical trial design might be something you for which JMP could be usefully used.
Q: How did you set constraints?
A; There are a few options. I used Uncoded constraints (raw units). another options is to set all your factors on a range of minus one to one then use coded units. Or you could ask JMP, for example and put in the two points that define these two lines (the upper and lower constraints). Then, in this example, JMP will solve, and you proceed from there to specify interactively. For advanced users, you can also apply domain expertise and put in equations for circles and ellipses, and you can get very exotic on your constraints, you get a more than one constraint, etc. There are also ways to set up inequality constraints that indicate unacceptable values (like never use this type of meat for a low-calorie pizza).