I don't know much about this topic but I will just give my little opinion. I think what the Dalai Lama is saying, by following the Nalanda tradition is what Lineageholder mentions in regards to the dialectic system that stems from the Nalanda institution, which is the memorization of a text, study and then debate. I actually found this to be one of the best ways to comprehend the meaning of a text. Even though still on an academic level, rather than an experiential one, the meaning still seems to penetrate further into the mind than using other techniques.
But what really confuses me, as Lineageholder, mentions is that His Holiness says much of the knowledge is not Buddhist but secular. I don't believe this one bit. Also, yes, many religious traditions have co-existed in harmony in India in the past, but there are very notable cases where they have not. It was Vajrayogini who spoke to Lama Tsongkhapa and told him to replace his red pandit's hat with a yellow hat, symbolizing the growth of the Dharma, rather than control. In my understanding Indian pandits wore red hats during debates with non-buddhists, symbolising the need to 'control' their mistaken views. Yes, Buddhism has in the most part been a peaceful religion, as according with its teachings, yet it has not and in certain parts is not accepting of other religions. There is no need to sugar coat it apart from if your motive, rather than expressing fact is in order to portray something else. Or perhaps even cover or deflect from the fact that His Holiness is schismatic, and not harmonious within his own religion, his own tradition....
