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.

There's no obvious datum to reference, for starters.

From bottom to top you've got the motherboard tray, standoff spacers, the motherboard itself, the socket, the CPU itself, the cooler, and finally the side plate of the case.

For most parts the top of the motherboard is the easiest reference. Motherboards are usually ~1.57mm thick, which gives the case manufacturer a pretty solid reference for the placement of the rear io shield, PCIe cutouts, and motherboard spacer length.

Now, the case manufacturer knows how wide the case is, so they know the distance from the top of the (expected) motherboard to the side panel. That's easy. But that's not the cooler height - you need to subtract the height of the socket and the CPU from that. How much is that? That's going to vary from socket to socket! Intel's LGA1851 has a stack-up height of 7.03 +- 0.5mm, AMD's AM5 is 7.98 +- 0.6mm. So currently it is anywhere from 6.53mm to 8.58mm - which isn't very helpful if you're asked to write a spec sheet...

So what is a case manufacturer to do? It doesn't hurt to have a bit of extra space, so you're probably going to have some kind of historic "maximum socket height" value lying around which you just subtract from the top-of-motherboard clearance to determine cooler clearance - as you have been doing for decades. It's not true but it's close enough, and nobody complains so why would the case manufacturer care? Or you physically measure it, and end up with a skewed measurement because you accidentally measured on a very thin Intel CPU / very fat AMD CPU.

TL;DR: Nobody notices because it is nontrivial to determine, and very few people care about squeezing out every last millimeter of cooler clearance.

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