You are correct on the spread spectrum clocks. Outside of military, they really soley exist for compliance (specifically unintended electromagnetic emissions) and are increasingly everywhere out of necessity. If an integrator needs spread spectrum locked on, there is no doubt a BIOS available that does just that.

"Now that I'm in position to ask ;)"

Ask away :) This is boring for 99.99999% of the population so I don't get to talk about it often :)

"I've wondered about the glass/plastic window PC cases.. Surely a PC case itself would not be required to have any emission tests done on it, or would it?"

You're right, a PC case itself does not need EMC compliance, but a PC case that's sold with a power supply does. So does one with built in fans and lights or anything electronic. IMO and very much off the cuff, certing the case + lights and fans without a whole computer inside is probably reasonable. But I would personally try cert with a whole PC (defence in depth).

"On the other hand, might the PC motherboard emissions be certified with the assumption that it will be placed inside a case?"

Yes it can be certed that way. Generally if it is, the details have to be in the manual.

But also, legally, you don't really need to cert a motherboard because it will always be integrated into another thing. However the reality of the PC architecture is that it is extremely modular and reach module is extremely complex. It's simply not at all practical for any systems integrator to try to modify those modules to try and make a whole PC compliant so that they can sell it. Even sticking the whole thing in a metal case might not be enough because the case has cables attached to and unwanted emissions and get out via those.

So for practical purposes manufacturers of motherboards, graphics cards, PSUs, hard drives etc vigorously test and cert their products with decent margins so that no matter what cards are used or how a PC is put together, the sum will be compliant. And this rule holds pretty well in general at all scales, from the individual parts and submodules that come together to make a product up to several products wired together in your house with power and network cables.

And system integrators can demand these requirements because it's necessary for the industry to function. I found a few years ago on Dell's website their manual for part suppliers. It listed every standard they required, made stricter and even had additions of their own so that they could sell with your module everywhere in the world, because they sell everywhere. It basically a thick manual on making a computer "world compatible".

"And then finally comes a consumer (or even a small integrator) and sticks in a PC motherboard inside a windowed case—but in this case the case might not be doing much on the RF side. Or maybe the cases provide better RF protection than they look like or the MBs don't need a case for that reason in the first place :)."

And the consumer benefits from everything I explained earlier. They can buy parts and assemble a computer that will be compliant. It's also why computer shops can build you a PC and sell without a cert and it'll be fine. Just the sheer effort of all these manufacturers so that they have a market to sell into means that the problem is solved for small players in the traditional PC world. The traditional PC industry is quite unique in that way actually.