square bore is the "traditional" Holley four barrel base plate design. It's called "square" because it looks square...if you turn over the carburetor, the silver grey piece with the 4 openings, which bolts to the manifold, is called the base plate.
Spread bore can be either the Rochester/Quadra jet design, where you have a different size set of bores. Two smaller bores (the primaries, are for cruising, economy) and two huge secondary’s (for acceleration). Then there is the 4500 Holley design, which took the regular square design and increased the size, about an inch. it still looks square, but it allows much larger bores for both front and rear bores.
The 4500 was designed to be a race carburetor, they can flow in the 1000 + cfm range, more than most 2X4 or 3x2 multi- carburetor set-ups from the 60's and 70's. (there are some 4500's now that supposedly flow around 750, but have the look of the big boys...gives you the “street creds” without having to learn how to tune or tame them for the street...Poser stuff?).
Most guys go with either the regular Holley or a few step over to the Quadra jet. Its mostly a preference thing.
However...Ford engines and Holley carburetors have been like peanut butter and jelly ... they seem to go together. Rochester/Quadra Jet has mostly been a GM thing. So, yeah, in a way there is a preference for some guys...the Ford vs. Chevy "battle" has gone down to carburetor too. Most people don't make a big deal out of it anymore.