They will work together, though they will not integrate together as well as if you stick with same brand combinations. The Total Control system is a chemistry automation, while the Easy Touch is an electrical automation system. They have very little overlap in features, only that the EasyTouch can optionally have a SWG added on.
A Pentair SWG can be controlled from the EasyTouch remote, while an AutoPilot unit needs to be controlled directly from it's own control panel.
By the by, I don't recommend getting the Total Control version of the AutoPilot unit on a residential pool. ORP based chlorine automation is very problematic and usually makes for much more trouble rather than simplifying anything. Their SWGs are great, but the chlorine automation is not suitable for residential users.