Yes I agree it is hard to get that 1/4" accurate even after measuring, remeasuring, cutting, sewing and poof it is short.
I think it is because when we press ever so carefully it still takes up some 'thread space' and shortens our qtr inch.
A friend told me her trick....yes use your qtr inch foot that has the guide (better than trying to eyeball it and the fabric shifts while sewing) but if you are able to move your needle right of center, do that, to get your scant qtr inch. I have a Janome that has a default of 3.5 at center, I click it to the right to 4.5.
Be careful when pressing so that seams are flat and don't have a tiny fold, the fold takes up more of your fabric.
When you square up, you will most likely just have a smidge to trim on all 4 sides. Sometimes mine actually come out perfect, depends on the quality of fabric and how much give you get when pressing.
don't know if this will be helpful for you, but it does work for me.
Good luck and happy quilting