You're trying to convert the 3D world as we know it to 2D, but there's no such restriction. There are other constructs in 2D that can be used for the same purposes.

Take Game of life for example. It doesn't matter that you cannot make circuits without crossing wires in 2D, Game of Life is turing complete anyways. A computer based on GoL is totally unlike our 3D computers, but can have the same capabilities. There's no reason to think that it would be any different with biology.

Or you can try comparing our 3D world with a hypothetical higher dimension. Our intestines are hollow cilinders, stable in 3D but not suited for 4D — in 4D you can look inside a 3D cilinder just like we can look inside a 2D-sphere (a circle) from our 3D perspective. A 4D creature would probably have a very different, more efficient, structure for this use case (food containment and nutrient absorption), which they probably wouldn't be able to just translate to 3D.