You are correct, the stock downpipe (DP) has two catalytic converters. There is a third catalytic converter in the uppipe.
You may or may not throw a Check Engine Light (CEL) if you go from the stock setup to the Invidia or any other similar pipe. When I installed my Cobb DP w/high flow cat, I didn't throw a CEL.
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'12 Prius Plug-in