And RTA can work several ways depending on the software or settings. It is a continuous signal that allows the user to take a snap shot at any given time or set a number of averages. You can typically set it to take 20 or 40 samples and average them.
A MLS response is a short duration signal that allows the signal to be viewed over time. Looking at the impulse response, the user can gate the time window and start just as the signal reaches the mic and stop it soon after and before any reflections can arrive.
Taking gated measurements on and off axis will tell you exactly what the speaker itself is doing.
Oddly, I often see RTA measurements made with both speakers playing at the same time. So you not only get room interaction, coupling, and cancellation effects, but the a compounded effect of having two sources playing the same signal in that same room.