that is rather interesting to learn of the rift that happened between the Panchen lama and the 5th Dalai Lama, and how he broke Guru devotion, perhaps that is the reason why the 6th Dalai Lama decide to manifest as a mahasiddha, and also why several of the Dalai Lama's incarnations died young, although they took the Panchen Lamas as their teacher again. But with that said, he probably wants to show us the dangers of going against our own Guru.
In all honestly, i do not believe that the current Dalai Lam is a fake incarnation, but rather he is just manifesting something different that what he is expected to manifest. After all, who are we to confine the Buddhas and enlightened beings to our own narrow thinking? If he was really the fake incarnation then Tibetan Buddhism would have never reached the USA and Europe. It is all thanks to the Dalai Lama's efforts, decisions and actions that the Dharma can spread so far.
The Dalai Lama cares more for the welfare of Buddhism as a whole, and not just for his own tradition. If he can subject Gelug to this, of all the traditions, it is pretty evident that he knows Gelug can take it, survive and grow bigger than ever. The harsh reality is that many people these days prefer to dwell on mystical experiences that nobody can verify and are adverse towards logic and reasoning because that dispels the oh i am so holy illusion that so many Buddhists cling on to.
I have heard of so many times, of people who have not heard of Lama Tsongkhapa or the Lamrim, even though they are Tibetan Buddhist. When asked they said they prefer Nyigma or Kagyu, but cannot explain why. They are just too afraid, in reality, to be questioned and to have their knowledge and views dissected and verified or backed up against logic, reasoning and scriptural basis. This is not the fault of the lineages or Gelug, but rather this is how Buddhist practitioners have became these days, and this ban seems to be designed to highlight Gelugpa in general.
Perhaps at this time, it is better for the Panchen Lama to not appear for reasons that we cannot see at this moment in time. I believe he will come back and lead Tibet when CTA has proven their worth as an independent government that will not depend on the Dalai Lama for every single decision, but rather do what every other government does: makes decisions out of cold, hard facts and not just out of hearsay and belief and implement more transparency in their administration.