I know exactly what you're talking about. It's the main reason I ditched the ceramic Subs. Lugs, crown guards, and slab side cases make them wear larger than the 40mm size claims. I felt a 116610/114060 wears more like a 42mm.
I've had a 5513, 16610, 116610, and 126610. The 116610 felt like the bastard child out of all of the Submariners. Proportions are all off, IMO. A 116610 and 16610 have the same height, but the slab side of the 6 digit case is thicker because they brought the case down to get rid of the groove the caseback sits on.
The newest 126610/124060 wears the flattest on the wrist out of all Sub reps available. It still wears large and chunky though, and the larger bracelet/clasp are noticable. The 14060m wears the thinnest and flattest of all the Subs, but it's never been properly repped, and a franken build isn't worth the effort IMO. (I'll be going gen for mine)
Here's a comparison between a 16610 and a 116610. The dial, crystal, hour hand, and crown are all the same size between models. It really shows how chunky the 6 digits are.
Also, notice that the ridge were the caseback sits on the 5 digit is absent on the 6 digit. The 6 digit case sides got thicker to get rid of it. The overall thickness is exactly the same.
(Gen photos courtesy of TRF)