There are currently two issues that seem to convince Beijing that ,though the Dalai Lama may be publicly declaring that he wants only autonomy for Tibet, what is happening on the ground shows otherwise
The first issue is that of the spate of self-immolations by mainly young Tibetans(including many monks),which have been allowed to go on and left unchecked by the Dalai Lama and CTA.The Dalai Lama and CTA have made no effort to stamp this out. One negative message being sent out to Beijing is that the Dalai Lama and CTA support these self-immolations which are being carried out in the name of the struggle for Tibet's independence. That means that, in reality, they support the struggle for Tibet's independence, despite the Dalai Lama's open declaration of support for the Middle Way/autonomy.
Another disturbing message is that the Dalai Lama and CTA support activities that have a high potential of causing social and economic instability. For Beijing ,rushing to contain this possible fallout of the spate of immolations in China, this is anathema to all their efforts to promote peace and stability and to contain unrest in China.
But what is more alarming for Beijing is to see how the ban on Dorje Shugden is creating a schism and a potential for great unrest within the Tibetan community. Judging by how the Dalai Lama and the CTA seem to be enforcing the ban,and the subsequent violence and unrest that ensued,Beijing must be wondering how far the Tibetan government can be trusted in terms of having a genuine desire for mere autonomy for Tibet for the sake of peace, stability and democracy.
The best way for CTA to assure Beijing that they are independent of the Dalai Lama and that they are a purely secular government, is for them to effect the lifting of the ban on Shugden practice, which is an entirely religious matter. If they can do this, they will be showing Beijing very clearly that they are no longer tied to the apron strings of the Dalai Lama, and that they have the political power and the will to act for the sake of peace for all parties.