You're talking about option routes...all offenses have that built in and yes the QB and WR need to be on the same page in those instances. What I'm talking about is completely off the playbook, like for instance the play calls for a go route, deep slant or deep out depending on the coverage and the WRs runs a button hook instead.
The issue of having a lot of option routes built in may be what caused Chad to struggle so much in New England. I think there were times where he just wasn't on the same page as Tom Brady and lets face it, Chad is not the smartest guy.