They have said that. I think Roy mentioned that sometimes Sakic has to move a bit, or Roy has to move a bit, but in the end they find agreement. That was exactly the quote that made me think they have equal power. Otherwise Sakic wouldn't need to be persuaded.
Also would Roy really accept being relegated to a lesser role? Doesn't Roy often personally handle trades? Sure, Sakic is the boss in title, but I think practically they have equal power.
I've seen it mentioned that both Sakic and Roy talk trades with other teams. I'm sure compared to nearly every other coach in the league, Roy has more significant Front Office power, but I still think that Sakic makes the final decisions on everything.
Perhaps the "move a bit" thing Roy was talking about comes when discussing players he really wants, so he fights really hard to make his voice distinctively heard, whereas Joe maybe has his own areas where he wants things done and makes sure his voice is distinctively heard.
I'm sure they get along, for the most part, but I have no doubt that if there was ever a situation where they were divided, and heavily so, that Joe would win out. Let's say O'Reilly is that situation. Perhaps Joe comes to the conclusion that they just can't make an extension work. That they have the magic # from O'Reilly's people, for what it would take to sign him, and Patrick believes that it's not only "totally doable", but that they should be drawing up the contract at that moment. But maybe Joe believes it's just not a great long-term solution, and he has a great trade offer on the table. I'm sure, given that we've seen how much Roy trusts Ryan, and how he uses him in almost every situation, that he would fight tooth and nail to keep him and to sign him, but Joe would win that argument if he passionately felt that they needed to accept the (completely hypothetical) trade.