Unfortunately it's not that easy in this instance.
Basically, what a remote start bypass does, is emulate a key in the vehicle. Most systems do this through a hidden key in the vehicle, or by physically splicing into the PATS antenna ring on the column and emulating the signal from the transponder key.
Using this type of bypass, still requires the rest of the PATS system to be in the vehicle. In my instance, that would require the Body module from the F150, as well as the transponder antenna.
At that point, I could just put the keys in there fixed to the transponder antenna and do away with the bypass system, as they would essentially do the same thing. When we turn off PATS as how Zach was describing, we hard code it off in the computer's software, so it never looks from the all clear to start signal from the BCM.
Unfortunately, at this time, due to the complexity of the EPATS system used on 2011 F150 and later, it's not that simple. SCT and HPT are working on a fix so people can use salvage setups like I am currently, but at this time there is no way to disable EPATS.
Ford offers the FRPP computer/harness for the Coyote, but it only supports a manual trans, not the 6R80 Auto.
I have a solution to my EPATS issue I believe, and am currently working with HPT's R&D team on the issue. I'll keep everyone posted when I get to the testing phase after the wiring is complete and we're ready to fire it up.