my guess is that you will no longer need to mods from ATP since those are meant to give you the ability to use a manual boost controller. It would be silly if the AP allowed you to up the boost but didn't change the maximum boost allowed by the ecu....
so in short, yeah, its pretty safe to assume that all you really need is the AP. Keep in mind that since its a reflash, it has the ability to change ANYTHING the current ECU controls. Just look at some of the neat stuff they do with subie ECUs, they put stuff in like launch control and fiddle with rev limiters to make flat shifting safer/easier... its some REALLY neat stuff!!!