I would assume by physical release they mean actual physical media as opposed to digital downloads. And I have to assume, at least in the case of PC games, they are updated to run on current generation operating systems. At least some of the games likely have updated resolution and possibly updated graphics. For example, I know Bounty Hunter is supposed to be the same version available for download on the PlayStation Store for the PS4 which advertises as “Re-experience Star Wars Bounty Hunter™ for PS2™ like never before! Featuring full 1080p up-rendering and offering enhanced features such as Trophies, Shareplay, Remote Play, Activity Feeds and Second Screen support for game manuals with ‘PS Vita’ or PS App.”
As for the NES thing, I bet it is an actual NES cartridge. But I don’t know for sure.
JEDIT:
They have indeed made actual NES cartridges…