That's a bit of a stretch of a claim though, at least in my opinion. Just because it leverages off the hardware capabilities more than the standard version of the software, doesn't necessarily mean it's a full fledged port. Quite a few Nintendo DS games leveraged off the Nintendo DSi hardware capabilities through real native code whenever you played on said hardware (Mario vs. Donkey Kong: Mini-Land Mayhem, Pokemon Black and White, etc.), likewise for some Nintendo 3DS games when played on a New Nintendo 3DS (Super Smash Bros. 3DS, Metroid Samus Returns, etc.). They were hardware enhanced software builds, all in one package. Nintendo Switch 2 Editions are very close to that design philosophy, except that here, instead of getting those enhancements in one build of the game, you are charged $10 extra to obtain the extra enhancements digitally, or you can buy a second copy of the same game again, just bundled with the enhancements. Basically, you are buying what would essentially be, the rest of the software code for $10 more lol. I guess if I had to put it another way, you are paying for a copy of Pokemon Black, but in order to have the DSi enhanced features, you have to pay $10 more via an upgrade pack or buying a second copy of the game with the upgrade pack bundled.
As for the whole "software being native" arguement, I guess it depends on how you look at it. If you look at it based on the principles of the upgrade packs giving you capabilities you wouldn't get on an original Switch, then sure, it's native. But native in this particular case to me means software that's built specifically and fully for the hardware. The problem is, Nintendo Switch software on a Nintendo Switch 2 is handled by a compatibility layer, meaning the software code has to be translated for the Nintendo Switch 2 hardware to understand, the code itself is limited based on the standards of the original Nintendo Switch hardware, and by extension, the compatibility layer in this case. These upgrade packs aren't full fledged Nintendo Switch 2 builds of the game(s), in fact they don't even make up half the size of the original software being upgraded. Considering a good portion of those upgrade packs also contain assets for higher resolution textures and what not, that means the amount of room left for native hardware code is even less than the overall advertised size. Unless these companies are wizards, I highly doubt the code present in the upgrade packs are even remotely close to being full fledged, native hardware builds. Take Metroid Prime 4: Beyond as an example, you really think the developers crammed a full native port in a ~1.5 GB upgrade pack, especially given a portion of that contains higher resolution assets too lol (the original game itself being ~28.9 GB)? If they were "ports" then that fine print on the bottom wouldn't need to exist, they would be full fledged hardware ports, essentially they would functionally be in the same rank as the standard Nintendo Switch 2 physical releases I have listed so far. The distinction is very clear though, and the implications are that Nintendo Switch 2 Editions are still Nintendo Switch builds of the game(s), just with additional enhancement code and assets sitting on top to take more advantage of the Nintendo Switch 2 hardware.