Playing people out of position has been a very "Metsy," thing to do ever since they tried to force Piazza to play first base. I hate it. I like J.D. a lot, but I agree - he is not a 3B. Also agree re: Dom. Making Daniel Murphy 2B kept his bat in the lineup, but his crappy defense was one reason we lost the World Series in 2015.
This goes back before Alderson's tenure, too. Phillips, Minaya, etc. ... same crap. For some reason the Mets' philosophy is always, "get great starting pitching and get good hitters, regardless of their primary/natural position." I don't like it and I hope it changes as Cohen gets settled.