There's nothing hypothetical about the relationship between matter, energy, and spacetime. It is measurable, definable, and demonstrable.
First, for the following discussion, let's simplify our universe/dimension to 3 dimensions, rather than the true 4, including time...just for sake of the discussion. So I will refer to our universe as 3 dimensions.
For example, let's take your Flatland analogy. That is a matter of perception.....two dimensional creatures will view a 3 dimensional object very differently. Let's think of Flatland as a piece of paper with little o's running around that are two dimensional people. If an apple passes through that two dimensional realm, they will see a red, irregular blob that appears, changes shape and mass for a little while, then disappears. They will never see the white interior, nor the whole shape representing an apple, they will just see a constantly changing blob.
That is perception, however, and has no effect whatsoever on physics. Two dimensional people will have 2 dimensional physics...whereas 3 dimensional people will have 3 dimensional physics. Right?
Those physics will AGREE!
To take a simplistic analogy.....in the 3 dimensional world, the Pythagorean Theorem (I know, it's geometry, but it keeps the analogy simple) is valid....
That is a two dimensional theorem in a 3 dimensional world. It will be identical in both worlds, yes? Einstein needed Euclidean Geometry for 3 dimensions, but Euclidean 3 dimensional geometry doesn't somehow negate the Pythagorean Theorem, it just adds.
2 dimensional worlds will simply LACK 3 dimensional physics. There is no need for it, and no way to measure things in 3 dimensions. So, your assumption, is that we in the 3 dimensional world will lack physics that exist in 4 dimensions. True.
But, 4 dimensional physics CAN NOT and WILL NOT violate 3 dimensional physics! 3rd dimension physics and 4th dimension physics WILL AGREE 100%. There will just be MORE physics in 4 dimensions to know and measure, but those 4th dimension pjhysics will
never, ever violate our 3 dimensional physics!
That means, that the speed of light is the speed of light. That means that the relationship between energy and matter remains constant, whether in 2, 3, or 4 dimensions.
E = mc2 in two dimensions, E = mc2 in three dimensions, and E = mc2 in four dimensions.
(EDIT: Incidentally, the "speed of light" is kind of a sloppy shorthand...it's not really true. What we are actually talking about is the "speed of causality", the rate at which information can travel through space without friction, thus the speed at which something in one place can influence, or pass information to, another. Therefore, nothing can exceed it...because "something" is information.)
To demonstrate that, consider the following thought experiment....
In Flatland, Flatlanders could apply enough energy to fold that flat piece of paper and "warp" from one end to the other, without travelling the space in between....they just fold the paper world. The residents cannot see the folded space or the fold, they just know that all of a sudden, the space in between disappears....they are going "faster than light".....but it takes X amount of energy to fold that paper.
Now me, ET Baron...I live in the 3rd dimension.....I can fold that paper world also....and to the Flatlanders, it looks the same....but I can perceive what is really going on, and they can't. This is the crux of your point, and here is the rebuttal......
it doesn't matter that my perception and understanding is better than the Flatlanders, what matters is that folding that paper takes a certain amount of energy, and that amount is consistent, whether the Flatlanders are doing it, or whether I am doing it from the 3rd dimension.
The Flatlander paper world's properties are inherent, they are universal, they are consistent. The inherent properties of that world do not change merely because the observer changes perspective.
Does that make sense?
If 4 dimensional physics are different than 3 dimensional physics, then we would observe very different physics in our 3rd dimension when we define 2 dimensions...and we don't. The formulae are the same, only simplified.
EDIT ADD:
To give another example...we ran with Newtonian physics for 300 years....and they worked, and they were valid. Einstein came along and gave us Relativity...but all that did was offer better understanding and precision to Newtonian gravity....it didn't alter, violate, or negate Newtonian gravity in any way whatsoever....it just refined it and filled in some gaps and inconsistencies. Newton's physics STILL WORK, and Newton's physics are still applicable in most situations.
Nothing will ever make Newtonian physics not work.
Nothing will ever make Relativity not work.
One day, we will have our Universal Theory that unites Relativity and Quantum physics....but nothing in that new theory will violate Relativity, just as nothing in Relativity will violate Newtonian physics.
What we know to be true and inviolable in physics, will remain true and inviolable.....because we didn't make them up ad hoc, we arrived at them by observing the universe.....the universe tells us what is true, not the other way around, and the unviverse tells us that C is C, the speed of causality is a core function of the universe, that which makes it work.
..and it's a good thing, because if the speed of light is violable, then we wouldn't exist....but that's another discussion.