The read option will be shutdown by teams like Seattle and New England, it's not a big deal against the quality teams. I doubt players would care if the better QB was put in, Romo was shown to be the better QB in the preseason, and his last healthy season was played at a far higher level than Dak can reach at this point in his career. I don't think players cared when Dez was put back in over Butler, same situation here. You play your better players period, if you bench better players, that'd be when I think chemistry starts becoming an issue.
Turnover wise, Dak has had 6 balls hit the defenders in the hands that likely should have been turnovers in the last 2 weeks, while Tony had 12 turnovers all of 2014. I think the rookie is likely to have more turnovers against playoff level teams, of which he hasn't faced many if any.