Pretty much. From all I gather, it looks like they (Rogers) wanted Duquette to take over for Beeston. With all the BS they unexpectedly faced with Baltimore, they were pissed off and finally managed to set their sights on Shapiro. Being so blinded by their frustration with Duquette and their excitement landing Shapiro, they probably didn't realize getting Shapiro on board meant letting AA go. So they told Shapiro to offer AA a contract (if he was cool with it-he said yeah) expecting him to accept/negotiate, were surprised when he rejected, but at the same time didn't really care too much because Shapiro is their guy and they would do it even knowing AA's "preferences".
The whole reduced autonomy seems like BS given what he's doing now. Really sounds like AA put up with working under/with Beeston, and given the choice of whether to do it again for 5 years with Shapiro said no.