I don't see where one precludes the other. I'm not a medical expert, so perhaps one of our verified posters could chime in, but I think it would be possible to be diagnosed with both. Perhaps she has some symptoms that are attributable to mito, while others can be ruled out as being caused by mito, and thus, point to somatoform. Say, something like lactic acidosis or relating to metabolic enzymes, those would be clearly mito, but other symptoms she's having may be better attributed to somatoform. Since we aren't her doctors, we don't really know.
In my opinion, I could see it happening. Justina is a very sick child. It's possible the stress of her situation could trigger somatoform, which would worsen her issues, given her symptoms of mito, and create the downward spiral we see now.
Perhaps it's not really a question of either/or - perhaps it's both, and that's why Tufts is back in play.