I just dropped my original 69 steering box out yesterday, it had four holes. From what little research I've done recently, it seems that most if not all first-gens have the 4 hole box for the reason Joe mentioned - many different applications. Dave Pozzi's website posted above is a great resource for anything steering/suspension related. Based on that, the centerlink not being parallel shouldn't be a huge problem, mine isn't parallel either.
1969 Yellow/black Std Coupe Camaro. GMPP Crate 330hp/350 + TH350 trans.