For the 700/800/900, there is also a statement to consider selecting ALT HLD in Mountain Wave activity and take the FMS out of the loop. Evidently that can improve A/T performance.
But the FMC calculates the approbate N1 regardless of A/P mode. I have not seen anything that even hints that the A/T response is different for MCP and FMC A/P modes.
There is a current bulletin concerning A/T response with certain software revisions such that if the thrust levers are idle in cruise for less than 60 seconds, response for the requirement for additional thrust can take too long. Amongst the recommendations is to not let the thrust reduce to less than 60% in the cruise and that CON maybe selected to help alleviate the lack of thrust at altitude.
The current Bulletins are in FCOM1.