Let's say the retail price of Windows is $200 and the normal wholesale is $100. So if I offer it to you at $20 a pop, provided you by a licence for every machine you build, is this a loaded gun?
Lots of small OEMs get buy without the deep discount.
They simply threatened to stop selling Windows to those OEMs at all. You're not going to sell many PCs if you can't sell them with Windows preloaded. This was especially true pre-XP when Windows needed to be severely tweaked for each individual configuration of parts that made up a given PC model. Very few consumers have the skills to perform these tweaks properly even if they wanted to.
These threats all went on deep behind the scenes, of course.