I think you maybe misread my post? Varys supporting Targaryens does make sense even with behind the scenes changes. Him and Ilyrio were plotting to get Drogo's army to attack Westeros, and at the time of their conversation Viserys was still alive so it can be presumed they are attacking with him leading. At that point they wouldn't have known that Viserys would ruin his own chances by getting himself skull-melted in the next episode, and that Dany would come forward as the stronger Targaryen leader. So now, after things in Westeros have unraveled even further it's not inconsistent that Varys would support Dany for the throne. In his convo with Tyrion earlier this season I believe he says he's supported the Targaryen restoration to the throne, not specifically the Dany restoration. He's been pulling strings for the Targaryen name the whole time, which checks out with what we saw in season 1, with him and Ilyrio working together to get Drogo's army for Viserys and pushing for them to attack Westeros.