First, why are you replacing the cats? They are a lifetime part (or until rusted out in the salt belt, or other collision damage, replacement needs). If you had a reason like an engine problem that ruined them, we might need more info.
Second, if you've taken it upon yourself to mod your vehicle, then why are you taking it back to the dealer shop? That's like doubly being a glutton for punishment.
What is the warranty on the cats? Why worry about it now? They either last as long as needed or they don't, at which point, what would the purpose be to pay a dealer to replace them prematurely?
Either way, what is the cause for the dealer to be assessing and telling you about your choice of cat manufacturer?
There has to be MUCH missing from your post, to know what's really going on, the back story behind this situation.
Is it still not running right? Did someone else tell you that the cats where the problem so you DIY (or had 3rd party) replace them, but then the pre-existing problem wasn't solved? What evidence lead you to replace the cats?
Ultimately, the ford dealer is going to tell you that nothing is as good as Motorcraft parts, installed by them. Sometimes they are right but more often, they just want you as their exclusive go-to shop, to make more money off of you.