Instead of using a line to the right of the needle to line up your seam allowance, mark to the left of the needle how wide that piece will be when sewn.
IOW - If you are sewing two charms together, instead of looking at that scant 1/4" seam, calculate the finished piece to be 4.75" and put something on your bed there. If you don't use the products made for marking beds, you can use a bunch of Post Its piled up, a cut up credit card, piece of foam... Whatever. Now let that be your fabric guide. Some of the outer edge of the pinking will be lined up with the 1/4" line you usually use for measuring, others won't. But after sewing, if you open up your unit and press as usual, you should have a 9.5" wide unit. Or if you are using 2.5" strips, put your marker at 2.25" to the left. When you sew two together, open and press, you will have a 4.5" unit.
Be careful that your seam allowance doesn't get to be too scant, but other than that, you should be good to go.