That plastic bezel is necessary because the body is too thin at that point to allow a 5-way switch to be mounted. I've never seen any successful mod that removed the bezel and retained the switch.
I agree with you that that plastic part sticks out like a sore thumb, particularly on a high-end guitar. Even the J. Custom S models retain that same ugly plastic bezel. I'm surprised Ibanez has never offered even a wooden version, which IMO would look slightly better.
The only S model without this bezel are the very early 540S models which had three individual mini-toggles to control the three pickups in place of a 5-way switch. This makes it a bit more fiddly to change pickups, but it also provides lots of versatility in terms of combinations and avoids the plastic protuberance.
https://vignette.wikia.nocookie.net/ibanez/images/2/2d/1988_540S_CB.png/revision/latest?cb=20161109224206