It shifts the threshold. so if I want things to be matched I need to do it for every FET, so its probably something to be avoided?

@Weston Braun You don't need to avoid it. Just have the same coverage on FETs that need to match. The shifts are in Vt and in mobility, and typically give you up to ~10% drain current difference with 100% M2 imbalance. H.P. Tuinhout, M.J.M. Pelgrom, R. Penning de Vries, M. Vertregt, “Effects of Metal Coverage on MOSFET Matching,” IEDM Digest_,_ pp. 735-739, 1996.