Thanks, I missed that even after reading the first quote and then again while reading the PHB. If it'd been a snake, it would've bit me.
What is it, exactly, that you're wanting to do? A specific question would give me a better chance at a concrete answer to satisfy you either way.
From the way you've phrased things, it seems like you want to take combat reflexes, then deflect arrows, and don't want to be flat-footed at the start of the round if your initiative comes up lower than the monsters'. Do I have that right? If so, I've already let you in on the secret that I haven't been (and am not likely to start at this stage) using the rule that characters are supposed to be considered flat-footed at the start of combat before their init comes up in the count, which may serve to make your concern moot. Other than that, about the only other time you'd be considered flat-footed might be on a surprise round. You can mitigate surprise by taking ranks in spot and listen. I don't know of a way to get rid of surprise entirely. If you do, please share.
Will taking combat reflexes and deflect arrows allow you to use deflect arrows while flat-footed? Not per the RAW as far as I can tell. Combat reflexes, per the SRD, allows you to react on instinct and grants an AoO while flat-footed. That's a whole lot different than using it for a defensive maneuver. Best I can tell, saying otherwise would be a house rule and one that I'm not likely to make.
But, again, if none of that was what you were wanting an answer for, then please do let me know.