This happens to me when I do woodworking - with wood, it's called kerfing, from the width of the saw blade. Your mark from the template will always be off by the width of the marker you use. Even if you cut and sew directly from your mark, it starts a whisker off. Multiply this by the number of parts you have used templates for, and over the width of a quilt you can be off a couple inches.
Strip cutting allows you to cut with only a margin of error equivalent to a razor edge. I would figure out the size squares I need to cut in half to produce 2 triangles at a time. I think for the long haul, it would be easier than trying to guess how many thread-widths you need to be over from your 1/4"