Well, yeah, that's pretty much why I didn't use it.
Depending on where you use it, it'll either increase your ember generation, or increase your Soul Fire burst. Neither of which is very conductive for figuring out the DPS differences between rotations. Testing the use of cooldowns in different parts of our rotation will probably be more useful when we're able to access level 90 content, and when our damage gets balanced properly.
Decided to kill two birds with one stone and did a test where I pooled 4 embers, and spent all my mana on Backdrafted Incinerates when they were up, or Fel Flames when they weren't. Except for two Ember Taps, all my embers were spent on Soul Fires when I'd pooled 4. Ended up with 21,369 DPS over ~5 mins.
I'm still not very keen on pooling 4 embers for burst unless I really need to. For one, over that 16 second total cast time it's really easy to cap Conflag stacks and mana. It's also easy to waste Backdraft stacks on the last few bits of that 4th ember. All three of those means wasted resources. For maximum efficiency, I'd rather build up about 3.5-3.8 embers, burn three on SFs, then build up that last partial with a Backdraft stack and pop a fourth SF. Backdraft lasts 14 seconds, so it's not going to fall off for one SF if I finish off that last ember early on a crit.
Overall, I'd still prefer to spend embers as I OOM, since that gives Backdraft some time to cooldown and I definitely won't cap on my other resources. I also won't take nearly as much self-damage. Doing maximum damage is important, but so is not killing yourself or overburdening your healers.
The main reason I'm concerned about mana is all of our ember using spells that aren't Soul Fire, though I admit that I haven't tested them as much. I'm not yet certain how reliant we are on Soul Fire's 4 second cast time for mana regeneration, so I don't yet know how our instant ember abilities would affect our overall DPS.
edit: I will admit though that I am probably being too conservative with my mana. As Destro on live I'm usually pretty blasé with the resource, and I'm probably overreacting to the loss of my Life Tap safety net.