I once had a Remington 870 Cerakoted after a house fire (lots of corrosion). They coated the interior and the exterior of the receiver, the forend tube assembly, the magazine tube and the barrel. Cerakote is a coating so it adds 1,000s of an inch thickness to all surfaces. After Cerakote was done, that shotgun was nowhere near as smooth as it used to be. Actually every single shotgun I've ever handled since then, the action has felt much smoother than mine. I don't know if they just did a poor job, applied too thick or if that's just the nature of higher tolerance parts with the additional mil thickness of Cerakote. It works fine, but just not what you would call 'smooth' with the action.
I know people here have more experience than me with Cerakote & M4 receivers. Maybe they could comment on whether it could affect the tolerances/action or not with your receiver. Without more info, I'd be more concerned with applying Cerakote to the exterior than all of the interior if that is possible.