After the post.align.trans, recenter tmat (design matrix).
(This is more expensive than centering zz, but it's necessary for eventual
tcov calculation to be correct.  The change should also correct the
calculation of the chisquare statistic.)
Edited a test for post alignment transform.  (Didn't understand the benchmark and was failing; replaced w/ wilcox.test as benchmark, and passed.)
When both stratum weights and a post alignment transformation are provided, I think users will expect the transformation to be applied before the the weights.  Modified to make this so.