The Two Places and Three Assemblies of the Lotus Sutra supports the doctrine of the Three Bodied Tathagata Shakyamuni who SGI rejects.

"Having thus undoubtedly regretted and reversed his previous teachings, he made clear his true intention, saying, “The World-Honored One has long expounded his doctrines and now must reveal the truth,” and “For long he remained silent regarding the essential, in no hurry to speak of it at once.” Thereupon Many Treasures Buddha sprang forth from beneath the earth and added his testimony that what Shakyamunihad said is true, and the Buddhas of the ten directions assembled in the eight directions5 and reached with their long broad tongues to the palace of the great heavenly king Brahmā in testament. All the beings of the two worlds and the eight groups, who were gathered at the twoplaces and the three assemblies, without a single exception witnessed this.

In light of the above sutra passages, setting aside evil people and non-Buddhists who do not believe in Buddhism, with regard to those who, though Buddhist believers, have devout faith in provisional teachings preached before the Lotus Sutra such as the Nembutsu, and devote themselves to reciting it ten, a hundred, a thousand, ten thousand, or as many as sixty thousand times a day without chantingNam-myoho-renge-kyo even once in the course of ten or twenty years, are they not like a person who, clinging to the transfer deed already nullified by his parent, refuses to accept its revised version? They may appear to others as well as to themselves to have faith in the Buddha’s teachings, but if we go by what the Buddha actually taught, they are unfilial people.

This is why the second volume of the Lotus Sutra states: “But now this threefold world is all my domain, and the living beings in it are all my children. Now this place is beset by many pains and trials. I am the only person who can rescue and protect others, but though I teach and instruct them, they do not believe or accept my teachings.”

This passage means that to us living beings the Thus Come OneShakyamuni is our parent, our teacher, and our sovereign. AlthoughAmida, Medicine Master, and other Buddhas are sovereigns to us living beings, they are neither parents nor teachers. Shakyamuni is the only Buddha endowed with all three virtues and to whom we owe a profound debt of gratitude. There are parents and parents, yet none of them can equal Shakyamuni Buddha. There are all manner of teachers and sovereigns, but none as admirable as he is. Could those who disobey the teaching of this parent, teacher, and sovereign possibly not be abandoned by the heavenly gods and the earthly deities? They are the most unfilial of all children. It is for this reason that the Buddha said, “Though I teach and instruct them, they do not believe or accept my teachings.” Even if they follow the sutras preached before the Lotus and practice them for a hundred, a thousand, ten thousand, or a million kalpas, if they do not believe in the Lotus Sutra and chant Nam-myoho-renge-kyo even once, they will be unfilial. They will therefore be abandoned by the sacred ones7 of the three existences and the ten directions, and hated by both the heavenly gods and the earthly deities. (This is the first of the five guides for propagation.) -- Encouragement to a Sick Person