This, to me, is the quality of Essence - the more you deviate from the baseline in appearance the more the general populace is unconsciously disquieted.
While I think the rest of your post is sound, I couldn't disagree more with this last statement.
Essence doesn't have to about appearance. You can get 5.99 points of bioware and look exactly like you did before. Essence affecting social limits is to my mind about that uneasy feeling you get in the pit of your stomach because the guy you're talking to just seems... off.
Again, as I see it a GM is encouraged to apply situational modifiers; the wared-out, cyberlimb enhanced, armed-to-the-teeth street samurai will likely go over with the Hollywood glitterati at the Holistic Humanity party like a pile of cow dung on the dinnertable, so it's a fair bet his dice pools might take a hit. But amongst street toughs who not only respect modifications but are also card carrying members of the Transhumanist Movement, his dice pool might very well actually improve. Note however that these are situational modifiers, and not what the game describes as the unknown factor that puts people on edge around low-Essence characters.
Regardless of situational modifiers, the fact remains that people DO feel uneasy around people with lots of ware, and this is represented by your Social Limit taking a hit whether the 'ware is visible or not. No matter how "in" or "out" you are with a particular crowd, you'll find it difficult to completely overcome the fact that you are, irrevocably, less you than you were before the surgeries. Of course, making an effort to fit in (i.e. wearing the right clothes, bumping some novacoke, etc) can make all of that easier.
Ultimately, I feel like this argument boils down to how each individual views the setting. I personally find transhumanism a concept that is easy to identify with, so naturally I'm less inclined to think of 'ware as something that stands out and makes you less human in ways other than that described by the core rulebook in terms of mechanics. But, I also agree with several posters in this thread that there is a lot of roleplaying opportunities tied to having (significant amounts of) 'ware; whatever that becomes, though, ultimately ends up being the players choice influenced by the world around him, which ultimately is the GMs domain.