I have a feeling the people buying the big box PC games aren't playing them. Playing those games in emulator or from Steam/gog just aren't very interesting to me. I want to play on an actual computer capable of playing them.
I also have a few (20-30) big box PC games and honestly I am not sure about actually playing most of them. This is especially true of the ones on floppy disk. I'm not certain how well that media has held up or how long it will last actually using it. At least I can say that I feel more comfortable finding the game online if I actually have it in physical form.
Your examples are top-end titles, it makes sense. But it may also be true that the reason why PC games have come down is just because you can buy them online. It is an ease of use issue, where people don't have to source a working old PC and battle with the compatibility nightmares of the day.
Presuming the used video game market doesn't crash, we could see a similar drop in physical media value if some service comes along where you can play PS2 or other games online or in some downloading fashion. I know you can sort of do that on Sony consoles, but that doesn't seem to have effected the secondary market yet. Time will tell.