That is how it works at the moment. The world server for Draenor is down, so I tested this on my alt, a level 90 priest.
Here's two screenshots, one of casting FH once, and one casting it twice. I'm completely naked so it's only the basic 10.4% mastery.
One thing you notice in the first is that EoL ticks twice, but in the other ticks thrice. Just doing the math, 10.4% of 1498 is 155.79, which is roughly the 156 healing(2*78) you see from EoL. In the other, the three ticks amount to a total healing of 312 over 3 ticks. 10.4% of 2*1498 is 311.58, so still pretty close.
What this shows however is that the healing from both FHs are incorporated into EoL.