Let's have a look at the graph again, with the caption. You see how it says increasing photons per pulse, and the total amount of photons emitted remained constant?

If you have a light on constantly, lets hypothetically say it emits 100 photons per second.
If you have the same light on half the time, it will obviously only emit 50 photos per second on average.
So say if you wanted the light off half the time, but want 100 photons per second, you could get two of these lights, or drive it at a higher current, which corresponds to giving off 100 photons per second.

If you have a look at the graph which shows relative luminous flux vs forward current for CREE XE-Rs, you need more than twice as much current to double the light output.

Conclusion: It's less efficient to pulse.

I can't make it any simpler.