Choose Assign Colour Profile in scripting - Select radio button

When the Color Settings’ CMYK Working space is the same as the document’s Assigned CMYK space, the radio button defaults to the middle Assign current working space. If your Color Settings profile is different then the Assign Profile radio button is selected, but in both cases the profile assignment is actually GRACol, and the only way to remove the profile would be to choose Discard (use current working space).

You could force the conflict with this:

app.colorSettings.properties = {workingSpaceCMYK:"U.S. Web Coated (SWOP) v2"}
app.activeDocument.cmykProfile = "Coated GRACoL 2006 (ISO 12647-2:2004)"

Which sets the Assignment dialog to this

Hi Selva,
not sure I understand – what radio button in the InDesign-native dialog is selected doesn't matter as long as the correct profile is assigned. And judging from you're screenshot the profile is correctly assigned.

Also important is what you set in your settings on PDF export. There would be another place where you could overwrite those settings.