you "don't" measure the seam allowance. You measure the blocks, stitched together, edge to edge after pressing.
I have dozens of 9 patch blocks I've made over the years on different machines, getting the exact 1/4" down. It can be different for all of us, some sew with the edge of the patch just under the foot, some like to see a thread of fabric beyond the foot.
Cut 1.5" strips, sew three together; pressed, do they measure 3.5" across? Exactly?
Then cut another three patch off those strips, and sew it to the perfect one you just stitched. Is it 2.5" wide? Exactly?
Now do it again so you have a 9 patch. Is it 3.5" square? Exactly?
I know where I like to see my fabric under the foot, so I mess with the needle right adjustment. Until It's Exact
It is well worth the effort!!! good luck, you can do it!