Perhaps trying to get intricate about the plot can sometimes lead to grasping at straws, but I don't think that's a bad thing. No one ever said that these theories were supposed to be what the writers intended. It's more like they are trying to make sense of the events that are presented, within the restrictions of the work itself. Often writers don't consider everything, and if no explanation is made by the author then I think it is valid to try to reason one. To use a good quote:

"A narrator should not supply interpretations of his work; otherwise he would not have written a novel, which is a machine for generating interpretations."
—Umberto Eco, postscript to The Name Of The Rose

They didn't have Playstations back then so just replace "novel" with "narrative." Anyway to add my two cents I do think that Sephiroth was the one in control, while at the same time he was executing Jenova's will. basically Jenova was the one with the goal (absorb all life) and Sephiroth was the one with the power (after he took control of Jenova) but it turns out he wanted to do the same thing Jenova wanted to do anyway. Considering that her will was passed on genetically it still holds up to say that Jenova's will was carried out even if Sephiroth was the one doing so. I think that's the extent of Jenova's control on him and I don't think the Ultimania's words are compromised by it. Sephiroth was basically an "evolved" form of Jenova. Not Like he literally evolved from her because his creation was artificial, but in the same vein. The reason Sephiroth is better than Jenova is because he can come up with plots like a human. Plots such as crashing a giant rock into the planet to make it gather all the life up and then hopping in and absorbing it. Jenova was more animalistic in her methods. So Sephiroth is the one calling the shots but he's still just doing what his biology tells him to, even if he wants the same thing consciously. Most likely it's a combination of both the influence of Jenova and his own desire for power. Either way Jenova wins. Until they both get a buster sword to the face.