I mean, on a molecular level there is no difference. I feel like they even did the whole ship of Theseus thing several times. And the obvious one is the 2nd Riker. Enterprise (the series, not the ship) saw the addition of transporters to starships and they talked about it a lot in that episode. Bones in the original refused to use them because he understood the science of it and knew people were essentially being killed and reassembled every time they were transported.
I always got the impressions that people who said non-replicated food tasted better were either deluding themselves or that extra flavor they attribute to the food is like, non food things in it. Leftover dirt, mold starting to grow.... Kind of like how completely filtered water is tasteless when the minerals and other fine particulates are removed. Transporters, as a side effect of how they work, remove illnesses from the body (Except when it needs to not for plot reasons. And don't get me started on the billions of bacteria that exist in our body all the time that are necessary for life that wouldn't count as "you"). So presumably, they would remove all those tiny things in food if transported, and obviously wouldn't create them in the first place if replicated.
While it's true that the writers made a point to learn nothing about the franchise before writing it, there's an argument to be made that at that point there wasn't really much lore from the games. It came out in 93. If today they made a game where Mario and Luigi from our world follow Princess peach through a portal to save her from being kidnapped by Goombas, only to find Dinosaur New York and get jump powers from technology, then you find out Bowser has usurped the Mushroom Kingdom power structure by de-evolving the king to the point of him now being a fungus who spends the entire game gently helping Mario occasionally... That would be an amazing modern day Mario game. Forget Galaxy, that would be the most complex and interesting game in the franchise.
Plus, it's got the funniest joke I've heard in any movie.
Desk Sergeant: Name?
Mario: Mario.
Desk Sergeant: Last name?
Mario: Mario.
Desk Sergeant: (rolls eyes) Okay, what's your name?
Luigi: Luigi.
Desk Sergeant: (exasperated) Luigi Luigi?
Luigi: No. Luigi Mario.
The whole movie is a masterpiece and the twist that the king was the fungus that's been choking the city is great, and on re-watches you notice all the times the Marios are saved or helped by the fungus. It also implies that the convergent evolution of this parallel world includes both dinosaurs and fungus turning into basically identical people, and the mushroom people managed to become the ruling class.