Will my square pad short if the pour isolation is too small?
Your PCB layout software makes the isolation circular as it only needs to isolate for the hole. The pad will only be made on the top layer and bottom layer. 
The hole is probably plated, but it will not generate a metal square on the mid layers (teal), so there is no need for a square isolation. When you put a pour on the outer layers (top and bottom) it will isolate for the square shape.