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.

On the other hand, other fabrials, such as Soulcasters, the Sibling, and Oathgates, are still visible in Shadesmar despite having a Physical presence

It’s also possible that their functionality requires them existing with a foot in both worlds, so to speak. They’re not dead spren nor typical living spren. They’re willfully imprisoned in some special way. Like, the Oathgate spren are the Oathgates, and seem like they’re more responsive, but we know it’s the same process as the Soulcasters and they’re basically inert. Sanderson has said they’re something like Shardblades, but he doesn’t say they’re just like Shardblades. They do act differently and affect things differently. Presumably they just work differently.

For point 2: I always got the impression that they did blip out when summoned. There’s hundreds of them out there, but they’ve had thousands of years. And while we view it as imprisoned, they say they’re keeping them safe (and from hurting themselves possibly I think, but I may be misremembering that bit). So they’re stopping them from wandering around by keeping them locked up, but it’s not trying to keep them all there forever. They just feel honor bound to take care of them. That’s their ultimate goal, not to round them up.

On top of that, I’m not sure, like Syl when she’s just being her little blue self hanging out with Kaladin is also in Shadesmar at the same time. I don’t think it’s like with lower spren where we’re getting a peek at them on the other side. I think they’re all the way over. Otherwise, in Oathbringer we probably would have seen Timbre, Ivory, and maybe Wyndle and Glys just hanging out on the cognitive side around Theylan City when Kaladin and the gang showed up. But it hasn’t been verified, so who knows? Sanderson is pretty good at coming up with good reasons for stuff in retrospect.