I think that when processing before the part is accounted for, the entire build platform is theoretically covered with the support pattern the cropped according the part's requirement.
So the pattern of the support exists before the part then cut by the part like a cookie cutter.
rebekah is exactly right. the support system works on a grid. imagine a piece of graph paper that represents the pillar locations. how big the squares are is the pillar size setting. when a part of the model covers a certain % of a square it is activated and a pillar is produced. it will never be the same from model to model since it just doesnt work that way. when you manually place the support you are just telling s3d that you would like support in that location and to activate a pillar in the grid. it doesnt mean that ever pillar you place will give you support exactly like you have it laid out.