Checking the "is a url" box under "advanced constraints" in the MARC framework/edit subfield section does not turn the subfield into a clickable link when viewed in the OPAC display. This happens (well, does not happen) with existing subfields and ones created for the MARC structure. This is either a bug or there's another step not explained anywhere I can find.
This preference has no influence on the XSLT displays, but only on the MARC display. It would be hard to impossible to do to fix that - you need to change your XSLT snippet to create a link.