Yep, I think you may be assuming things. It's been a while since I worked on either an LCRU or LCRU2 engine, but I thought the LCRU2 had the same issue. FWIW, I had an LCRX in a hot box Reefer to give it TMCC control, though I was pretty smart. It worked a bunch of times and one day it wouldn't work! It has the same polarity issue.
I'll wait for the final returns, maybe the LCRU2 doesn't swap the polarity, but I thought it did.