First of all, I am an engineer and very analytical and picky about my tone. In my experience, there was no audible improvement of the E string when going string through on my Jazz. The thinner strings sounded SLIGHTLY better, though.
I think the "witness point" argument/contribution will be offset by a bigger cross section string. In engineering, distribution of load is paramount in stable, durable design. The tight radius over the bridge will create internal tension and losses in the string, and there is an internal element that will strive for the string to move out, away from the pickups and body. The thick string would tend to remain LESS in the ideal witness point.
So your observation about increased motion might be reflecting that!