Just to make sure I understand -
You're adding an external overflow box to the end of your tank that will be 12" long. (I assume you have an internal weir in the tank with some holes for water to flow into the box) You're looking at drilling 3 holes in the bottom of the overflow box but are concerned about the proximity of the holes and so are considering using 3/4" plumbing instead of 1". Correct?
The general guideline for holes clearance is 1.5 diameters between glass edges with 1 diameter being the minimum. (
http://reefcentral.com/forums/showthread.php?p=23227315) For 3 holes placed side by side, the overflow box would ideally be 9x the diameter in length (minimum 7x,) and 4x the diameter in width (minimum 3x.)
A 1" bulkhead needs a 1.65" hole and a 3/4" bulkhead needs a 1.3" hole. Using these dimensions you have an ideal box length of 14.85" (minimum 11.55",) and an ideal width of 6.6" (minimum 4.95") for 1" plumbing, and 11.7" (9.1") in length & 5.2" (3.9") in width for 3/4" plumbing.
How much flow will you have? A 1" siphon can theoretically handle about 2000 GPH. A 3/4" pipe close is closer to 1300 GPH. The bigger issue will come with the open channel pipe. It essentially works as a durso, providing a range of flow over which the system operates silently and therefore determines the extent to which the system can auto adjust. A 3/4" durso has a much smaller capacity than a 1" one does. If the size is a concern you may consider having the open channel pipe 1" and the other two 3/4". You could also have 3/4" bulkheads and then upsize the pipe.
Another option would be to make an acrylic overflow box. You would have to use bulkheads and a gasket to clamp it onto the tank, but you wouldn't have to worry as much about the clearances.