yes to all the things Bear said and would like to add ...
.... it also depends on the thickness of the fabric you are using (especially if you are ironing to one side). An Asian print for example, will require a smaller seam allowance to get that 5" square she described, and a batik will require less. If you are using fabrics of various width's in your project, you will get various results
It will not make a whole lot of difference if you are making blocks using large pieces - say a 9 patch with 5" squares. But if you make small piece blocks (like me) it will make a LOT of difference.
Lastly, the size of the seam allowance may or may not make a difference BUT it should always be uniform. If your pattern calls for pieced border - then the size of the quilt before the border needs to be accurate which means your seam allowances need to be accurate. If you are putting on a solid pieced border you're going to measure it anyway so the quilt size can be whatever you want it to be.