From the little I am aware of Tantra (Buddhist), theory usually tend to be much less "physical" compared to the Taoists and rather use chanting, visualization and other religious methods to cultivate the "winds". Moreover, they tend to be dependent on deities, spirits and other beings for the cultivation of their life-force.
Vajrayana methods are certainly not dependent on any spirits.
Yet, it appears that most Tibetan Buddhist Yogins find it difficult to reach high levels of control over the winds even after many years of secluded retreats and practice. Compare this with the Taoists or practitioner of Taoist-derived arts. Even a martial artist will be able to open microcosmic orbit within 100 days if he practices regularly and naturally for the same time period.
Yes well, the goal of a Vajrayana practitioner is Buddhahood, not just some cultivation of "life-force". So what is opening the MO in comparison? Nothing.
1. Is there at least a conformity between these traditions with regard to the theory of human body, its channels, the Qi/prana/winds etc or they are completely different from each other? Since both the traditions deliver what they offer, it seems that the theory - i.e the channels, meridiens, five organs etc - are similar, if not the same.
I suppose you can find similarities but they're not the same.
2. Are Taoist methods superior?
Again, Vajrayana methods lead to Buddhahood. How could Taoist ones be superior?
On the other hand, Taoists and martial artists, who have also volunteered for such experiments, usually showed much better control of their Qi.
This is the first I heard of it. Tibetan practitioners became famous for their tummo done in labs, never heard of any Taoists doing something similar.