I think it is pretty simple. Similar to when triple engine airliners used to be commonplace, the third engine is used to both increase maximum takeoff weight, and as a cruise engine. During cruise you need less thrust and you can disable the outer two engines. Possibly also close down the bottom air intakes for reduced RCS.
I think the highest thrust requirement is when it goes supersonic.
Consider the possible operating conditions for the J-36 engines:
1. Takeoff
2. Cruise speed to area of operations
3. Loiter
4. Supercruise (3 Engines on Dry Thurst)
5. Maximum thrust (3 Engines on Afterburner)
I'd say 4+5 makes the most demands on the engines, as you want to be as fast as possible because these are combat conditions.
For 3, they should be able to use just one engine for loitering
For 2, I reckon they would need two engines for high subsonic/supercruise?
But maybe just 1 engine if they accept a slower speed. Incidentally, that would solve the coordination issue if the J-36 is accompanied by slow subsonic CCAs
(Note that in a two engine setup like the USAF NGAD, you can't voluntarily shut down an engine to become more fuel-efficient)
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But ideally, you would still have airflow and the engine fans running on the non-combusting engines.
So the fans continue to push airflow out of the engine and generate additional thrust.
In effect, you end up with a higher airflow bypass-ratio and therefore efficiency.
So it's another way to achieve a variable cycle engine?
But I expect this would be a future development.