I have a spectrum analyzer with mic and have used it on my stereo. Even though it's fairly expensive, I don't think it's capable of making enough EQ correction to make a room flat. But, I think the concept of flat is a good place to start, acknowledging that it may not be achievable in a practical sense. I can't imagine that any of my bass rigs come close to being flat and I've had some expensive three-way systems. As others have stated, once you're in another room, you start over again.
Having gone that route, I now find myself learning to appreciate what makes an individual rig sound good and it's NOT in its capability of being flat. I think if I were to play through a favorite rig with an EQ that satisfies me, that it would be far from flat.
So, for that reason I believe what is important is that I listen enough to determine what my rig is capable of, AND what it's not. And, using that experience to find the best tone I can get in all possible environments. With time, I have discovered that I don't use much EQ, or at least change the knobs, in any of the rooms I play.
More and more I think it's all in the hands and the ears.
Gale