I think the bottom line is - as others have said - is the finished size of the patch within the block the expected size?
Factors other than the seam allowance:
The size the pieces were cut - ruler placement, using a die cutter, using a June Tailor thing, did I cut around a template, etc. could make "my" 2.5 inch strip be several threads wider or narrower than "your" 2.5 inch strips/squares.
If fabric was not shrunk before cutting it, did it shrink while it was pressed during the piecing process?
The whole idea of a "scant" 1/4 inch seam annoys me. But I think the pattern makers put that in to discourage the use of "generous" 1/4 inch seams, which could really skew the results of a complex pattern.
When in doubt, doing the three strip test with the thread and fabrics intended is worth the time. Even within the "quilting cotton" category, some fabrics seem to be heftier/bulkier than others.
For me, the fabric preparation (preshrinking by soaking in hot water and then washing it gently) and the cutting are extremely important steps in the piecing process.
I know that when I cut - either around a template or with a ruler, my 2.5 inch strip is actually a couple of threads wider than 2.5 inches.
I do not have a die-cutter, and have not used the June Tailor strip thing, so I do not know how those pieces measure.
Are they "exactly" the measurement or are they a "bit bigger"?