Can the factory tune them slightly different to make more top end out if the same engine without infringing on gov standards and whatnot?
It may be possible in some instances if one of them is artificially restricted, but it's really challenging to achieve this otherwise. Cam timing, compression ratio, etc, everything that affects power output, also affects emissions. The MT07 is not artificially restricted. It makes what it makes, when you ask for 100% throttle that's what you get, there's no "restrictor plate" or artificial throttle stop.
In the aftermarket, there are things that can be done ...