It depends on the reference data, case companies are of course good at measuring these things given everything that needs to match up when building a PC to begin with. Therefore I would assume that case manufacturers measure it but add on an amount for assured clearance.

However of course it matters for Noctua as they want their coolers to fit and be assured they can fit into common/popular cases.

My thoughts are that if you take a case and a cooler, the assumption needs to include AMD and intel sockets and potentially multiple different generations of both that may have a sizeable difference in height between each other. Unless you take your measurement from the thickest of those as a safety net. A quick Google says that they can vary between +/-3mm typically.