Or even Sega Megadrive/Genesis versions, or ZX Spectrum if that was the best version of a particular game, which can happen on rare occasions? (i.e. Trantor the last stormtrooper)

Typically the Amiga version had better graphics and sound than PC if you are looking at games made in 1988 to 1991. A lot of PC games in this period were running on EGA and used the primitive onboard sound chip. And the early adlib music could have it's charm, but for sound effec ts it was not good. I would love for the Amiga version of North & South, and Centurion Defender of Rome (Cinemaware) to be brought to GOG.

They would have to come with a bundled in emulator, perhaps with every game so it can run seamlessly and it would raise the price, but even if it were an extra 5 dollars per game I would pay it in order to replay the golden oldies in the way i remembered them.

The best version of Trantor is the Amstrad CPC version.

And there are some amiga games here available:

https://www.gog.com/en/game/rocket_ranger_emulated_amiga_edition

https://www.gog.com/en/game/wings_classic

You're right about Trantor, never saw the amstrad version of it to be honest but it looks pretty great! Leagues better than the PC versions, and better than the Spectrums.

One thing though, if we have some Amiga emulated editions of games here on GOG, why do we get the objectively inferior PC versions, all so often? (i.e. North & South). They should use Amiga, or what is considered to have been the best version of these old games more often. Blade Warrior could be another example, the PC version was ok graphically but the sound was horrible while on Amiga the sound was pretty decent.

I don't know a definitve answer to your questions, but maybe there are different rightsholders for the other versions. Or the rightsholders/GOG don't see a market for these versions.
Maybe you should contact the publishers directly.

The Remasters of the classics Saboteur 1&2 could be of your interest:

https://www.gog.com/en/game/the_saboteur

https://www.gog.com/en/game/saboteur_ii_avenging_angel

"9 retro graphic modes: ZX Spectrum, Commodore 64, ZX-81, Amstrad CPC, Atari 2600, Gameboy, Acorn, NES, Amiga"

Short answer:

Different versions or ports of the same game almost always have different rights holders, which need to be individually tracked down, approached and asked for permission to redistribute the Amiga version for example.
Unfortunately these rights holders more often than not cannot be tracked down, have gone out of business or simply are not willing to have these Amiga versions/ports sold again.

On top of that you'd also need to make a deal with the creators of emulators like, for example WinUAE, in order to have the Amiga versions/ports bundled and sold with it.

And there's of course the Kickstart software.
I don't know what they did for Wings and Rocket Ranger, but if you use a Emulator like Win-UAE or FS-UAE (my favourite), you also need to buy a Kickstart file.

I would be down for the Amiga version of desert strike

No, UAE is Free Software, as in open source, as in GPL (GNU Public License), it can be used commercially, no need for a deal. Or at least that's my understanding, about how it works. The kickstart software on the other hand, that could be an issue, but I see GOG already has some Amiga games so maybe not.