this is a very interesting piece of news that I chanced upon while i was searching for some information. Why would the CTA want to make such a move? Is it because they lost faith towards their own tradition and insist on doing something like that? Mountains is right, there is nothing wrong with the Guru Rinpoche statue, but to have it forcefully placed in the monasteries' main altar is strange indeed. Why not force the Sakyas to do the same in their monasteries or is it because they cannot enforce such a thing on them?
or perhaps, this could be the karmic repercussion of the forceful conversion of several Jonang and Kagyu monasteries into Gelug when the 5th Dalai Lama came into power? Phegyeling monastery used to be a Kagyu monastery before it was converted into Gelug, namely and probably due to its location. the current HHDL has already admitted that most of these monasteries were converted due to political reasons and not for spiritual reasons. Perhaps there is some truth in this, as this act is being force on by the monasteries?
There isnt a difference between Guru Rinpoche and Tsongkhapa, of course, as this book here would highlight:
http://books.google.com.my/books?id=bXAUkoM0esMC&lpg=PR15&ots=wq4eqU_IU2&dq=shabkar%20vision%20of%20tsongkhapa&pg=PR15#v=onepage&q=shabkar%20vision%20of%20tsongkhapa&f=false that Shabkar's vision of Guru Rinpoche told him directly, that it was Guru Rinpoche who taught him the Lamrim as Tsongkhapa when Shabkar lamented that he was unable to see Guru Rinpoche after practicing him for so long. Guru Rinpoche told him that he had come the day before as Tsongkhapa. This shows that they are one and the same.
Therefore, other than for political reasons, there is no reason for such an unnecessary act as Tsongkhapa and Guru Rinpoche is inseparable and one and the same. I find this move by the CTA stupid, unnecessary and a direct indication of their lack of faith.