So, I tested my lens again and what I was hearing had nothing to do with the focus limiter setting. I am hearing the image stabilizer when it's active, but the sounds is being conducted through the body. I never noticed it on the Mk II, so I slapped it on my EOS film body and I can hear it there too. It sounds like an old floppy-disk drive when it was seeking. I'm wonder if the Mk III body conducts sound differently or if I just missed it on the Mk II though I find that kind of hard to believe.
Anyway, none of this is affecting performance in any way.