Not sure what the OP is talking about regarding it being slower - but I can say that on a TURBO vehicle, the larger the exhaust (especially starting at the turbo), the better. This talk of a dual 3" exhaust making the vehicle slower is silly. If one wants to argue that it's not any faster, then okay, I'd potentially agree to that. But to say it's slower...no. This is not a naturally aspirated engine where exhaust scavenging is a thing. Turbos love big open exhausts. Full stop.
Backpressure, scavenging, pipe diameter and velocity - all that stuff matters...on a N/A engine. Once a turbo is added to the mix, all that other stuff ceases to be a thing. Because the exhaust is no longer necessary to help suck fumes out of the cylinders. We have good 'ol forced induction pushing it out for us. And the turbo turbine, in order to spool free and happy, wants as little restriction as possible after the turbine housing.
Now. Assuming the OP is correct in that his vehicle is actually slower - if that's the case, then the situation is more likely that the factory tune is getting readings from sensors that it doesn't expect. Maybe the turbos will spool a little better, or maybe the O2 readings are a little off now due to the larger pipe size...I dunno. But what I do know, is that a dual 3" exhaust, or a quad 3" exhaust, or no exhaust at all, is a-okay and your turbos won't mind one little bit.
Does the stock exhaust flow good enough? Perhaps. I'm willing to bet it's a little restrictive because Ford has to deal with the EPA. But I don't have any facts or specs to back that up, so it's just me talking. Will a 2.5" dual exhaust or a 3" be better? Maybe. If you only ever stay at stock power levels, then arguably they are wasted money (unless you are doing it for the sound). If you ever plan on getting a tune, then no, the stock exhaust most certainly is not just as good nor is it better.