answer your question on the tune: I use a custom calibration from AJP Turbo (you can also look Unleashed) specifically to handle the PPE straight pipes contact AJP. These tuners can "silence" the rear O2 monitor logic so the light stays off. Fair warning: This will usually keep your Emissions Readiness monitors in a not ready state, so if you live in a state with OBDII plug-in inspections, you won't pass without functional cats.
Regarding your situation: the fact that you have both P0420 and P0430 makes O2 sensors highly unlikely. It’s rare for two sensors to fail simultaneously. It almost always points to an upstream issue affecting both banks or chemical failure of the cats themselves.
1. TSBs
Ford has released several bulletins for the 3.5L EcoBoost regarding catalyst efficiency. You should mention these to your mechanic:
TSB 14-0102: Specifically for 2013-2014 Taurus/Explorer. It acknowledges that these codes can trigger and mandates replacing the affected catalyst and performing a PCM software update. Even if you are a 2016, the software logic update is often the fix.
TSB 14-0017 / 13-8-1: These deal with the "Intercooler Moisture" issue. If your car ever stumbles under hard acceleration in humid weather, it's sending slugs of water/unburnt fuel into the cats. This kills the chemical substrate.
SSM 44521: Deals with oil consumption from the PCV system (that "PVC" thing you mentioned). If the valve cover/separator is faulty, oil enters the combustion chamber and "poisons" the catalyst, making it look dead to the computer even if it isn't clogged.
2. The Cat Count
If you go the replacement route, you have three total, but only two matter for the codes:
Primary Cats (qty 2): These are integrated into the downpipes directly off the turbos. These are the only ones the computer monitors.
Secondary Cat (qty 1): This is in the mid-pipe before the resonator. It is unmonitored. You can delete this one without ever seeing a light.
3. Tests
Since the car runs normal, the cats aren't physically melted/blocked yet. They are just chemically inefficient.
Temperature Test then have your mechanic use an IR thermometer. The exit of the cat should be roughly 100°F hotter than the inlet. If they are the same temp, the cat isn't "lighting off."
Spark Plug Gap: You mentioned factory gap double check that. For the SHO, we usually recommend .028". If you are at .033" or higher, you risk micro-misfires that dump raw fuel into the cats killing them.
Don't just throw parts at it yet. Check that PCV valve and the intercooler for "gunk" first. If the engine is dirty, it'll just **** the new cats you buy too.
Last thought, did the car get tuned and leave you with the problems of the light on?