Is it allowed (also considering sandboxing) to have your app bypass the system print dialog and directly talk to the printer when you want to publish it through the Mac App Store?
I know that you should use the system print dialog wherever possible. This is a for a special app with special color management requirements, though.
If you're only using public APIs and there's no specific guideline forbidding it in the App Store submission guidelines, then I imagine it'll be OK - especially since you have a specific reason to.
If it's not mentioned in the guidelines, you're going to have to suck it and see by submitting it to Apple.