As I understand it, the Doctor's old friend Padmasambhava supposedly contacted the Great Intelligence on 'the astral plane'. Perhaps such contact transcends the boundaries of time and space?
We certainly know messages
can be sent telepathically through time (The Hand Of Fear, Silence In The Library, The End Of Time Part One). For me, it's not such a leap to accept the Intelligence, banished in 1892, could be contacted by the wandering meditations of a Tibetan Monk in the 17th century.