It feels a little unintuitive, because the part is a square tube, but you can use the function Circular pattern. Select the holes on one plane as elements to repeat, select 4 repetitions and as turning axis the axis along the tube, then the holes get placed in the desired fashion.
After playing around a bit with Content Center parts in Inventor, I managed to reproduce your problem and find kind of a workaround. It is not as smooth as just typing your parameter name in the Content Center window, but maybe it helps you.
Place the part that you need with an arbitrary length in your assembly.
Rightclick and open the part (don't click ...