I'm using the Nexus as an example, how do you change it's placement size?
IE from 5 x 5 squares to like 3 x 5 or 3 x 3

I do stuff and thingies... Try widening and reducing the number of small nooks and crannies to correct the problem.
Chose a proper footprint or duplicate the footprint and edit it.
A structure has two footprints, one for the placement of that structure and one that it applies when it is built (for collision).