Good luck 'wearing down' one of those locking nuts. My main guitar is a 1990 RG550 with the original nut and it's still just fine.
And I used to really abuse the vibrato on my guitars, to the point that I've broken one of the OE trems many years ago, so if I was going to wear down a nut...
What do you mean by 'neck movement'?
has an Wizard II neck with a 400mm radius, and if I'm not mistaken' the standard Ibanez Top Lock has a 430mm radius (the larger the radius, the flatter the neck) and this may be what you're feeling.
The radius of the nut doesn't match the fretboard and it could just be it seems more pronounced on the B string, depending on how the nut is shimmed.
If it's not buzzing when you play it open, I wouldn't worry about it much.
You could also check at the bridge side and see if it's uneven at that end, since you can shim the individual saddles on the bridge you can easily compensate for the mis-matched radius a bit. It won't be perfect, but it can help.