It is not clear what you want to do but mach_inject is a way for user apps to interface with the MAC OS kernel using the Mach ports it is not relevant at all to IPAs which are essentially an archive - similar to zip or Tar.
I suspect that based on what you are describing that you have a library that you want link edited / included in a user app but you don't want them to see your source code and vice versa. I am not familiar with Mocana but based on what you described it uses an IPA for distribution, that is entirely possible, but so is using a precompiled object module which is what Facebook SDK gets distributed in.
In anycase, prior to distribution whether by enterprise distribution server or the app store, the entire package needs to be signed before the devices can download and run it.