The "logic gate" depicted isn't a real one, just and approximation.
This abstraction is all fine and dandy, but we can't forget about timings. It is absolutely crucial that two components (of the same base unit size) take the exact same amount of time for all inputs.
So, the compatibility issue between the current "cross-shaped" gates and the wire crossing is, once they've been made the same size as to be tileable, they will not take equal amounts of time.
Although there may be an option: put the current wire crossing in the center of the square, and pad so wires so that the I/O matches up with the square edges. Then, we must introduce a comparable delay into every other "unit" logic device.
@El'endiaStarman At least basic logic gates, wire crossing, and a clock or two the appropriate size (unknown until we figure out what sizes everything else is).