Only other thing I'd add is the neck joint crack in your first picture is INCREDIBLY common, and is almost always superficial, and just limited to the finish. I'll have to check the guitars I have at home, but I feel like most Ibanez guitars I've played have one, and I wouldn't be shocked if my '97 Strat has a crack there, too.
The trem route looks more like a design issue than a QC one - these are CNC'd, so if the route seems a little too big for the trem, that's an issue with how it was programmed and not executed. The slightly crooked neck pickup isn't really awesome looking, but won't impact how it sounds, and if you really are concerned you could fill and redrill the screw holes easily enough. Most of the issues you're pointing to are cosmetic in nature - how's the fretwork? How's the neck relief? How's it play? How resonant is the guitar? Does it sound good? For better or for worse, I think expecting a $1000 guitar to be cosmetically flawless probably isn't realistic - anything coming off a production line could potentially have minor cosmetic issues, be it $1k or triple that. It'll have a whole hell of a lot more in ten years after a decade of wear and tear. I'd say as long as a guitar sounds and plays great and the cosmetic issues are fairly minor, I wouldn't lose any sleep about it.
