The historian said that was because she "took one sort of society, and turned it into another sort of society". He picked her victory over the mineworkers as a key moment.
He is assuming that this is the definition of a great prime minister. I think that having a vision and imposing it on the nation is not necessarily in the nation's interest. If you accept his criteria for judging prime ministers then Atlee and Thatcher score well, but if we had lost the war or returned to appeasement when France fell, then Maggie and Clem could have had as many visions as they wanted, they just would not have been able to put them in to effect. For that reason, ranking them above Churchill is flawed.

As for a state funeral, Atlee did not get one so Maggie shouldn't either.