Nearly all Nintendo 64 games can now be recompiled into native PC ports

What saddens me is that open-source OSes do not want to provide a common set of APIs so that the developer only has to write and test the code once and it works everywhere. There is flatpak, but as I understand, it doesn't provide a set of APIs, it simply packs a Linux distribution into a virtual machine without any specifications or documentation. So ugly, and no compatibility for smaller non-Linux OSes.

Nintendo has, in fact, sold the public ROMs before (and I don't just mean custom emulator executables wrapping ROM payloads that get delivered encrypted onto DRMed consoles.)

Specifically, I'm talking about the NES Classic and SNES Classic. These little boxes use multi-image emulators, rather than Nintendo's usual approach of a customized single-image emulator for each game. And the ROMs used by these systems are just sitting there as files on disk. The disk isn't encrypted, either; nor is the bootloader or kernel integrity-signed; or really anything like that. You don't need to "jailbreak" these things — they act like Android phones, where you can just reboot them into restore mode and plug them into a computer with a USB cable, and see a virtual disk. The "modding tools" for them just drop a new kernel with wi-fi support into their /boot partition! (And you don't even need to go that far to read the ROMs off the rootfs — any Linux PC will work to mount it.) So any DMCA "they used DRM, which means their intent was to license you X, not sell you X" arguments don't apply. They did nothing to stop people from extracting these ROMs.

By buying these systems, you're effectively buying "a box full of ROMs" directly from Nintendo (the IP rights-holder for said ROMs), at retail, as a "money for goods" transaction. So now, by the first-sale doctrine, they're your ROMs, and you can do with them as you please.

This is true as surely as buying a DVD box-set means you now own those DVDs, and can do with those as you please. (Part up and resell the DVDs individually? Sure, why not!)

Or — for perhaps a more interesting example — as surely as buying a stock images or sound-effects library on CD (even second-hand!) implicitly brings with it the IP rights to use those assets in derivative works you create. The primary-market purchaser didn't have to agree to any kind of license terms at point of sale? First-sale doctrine applies to that IP from then on! (Amusingly, Nintendo redistributed exactly such stock-image CD assets embedded into Mario 64 — so their lawyers are double-bound to agree that this particular interpretation of first-sale doctrine should pertain.)

Console makers will often hire lead developers of open source emulators to sew something up for them, like what was used for the mario 35 collection (part of galaxy was recompiled too) or the "ps2 classics" software emulator for the ps3.

This is wrong. Please do not confidently present your guesswork as fact.

If it were true, copyleft would have no chance of working; binaries compiled from copyleft-licensed source-code would not be subject to the copyleft licence.