My thoughts on it are that it's a lot like The Yellow Rabbit from Into the Pit. Glitchtrap has Afton’s memories, personality, remnant and agony. But it's not him, it's an imperfect digital clone created by The Mimic's programming after scanning Scraptrap's circuits. A "MimicAfton" if you will. He probably also possesses some of The Mimic's agony and memories which is why he knows about Tiger Rock. So he's not entirely either.
The TLDR version:
Afton: Springtrap and Scraptrap
The Mimic: Tiger Rock and the other costumes in Ruin
Glitchtrap: Hybrid of both, Glitchtrap and Burntrap.
That's just my 2 cents on it. Frankly I just wish we could move on from this saga. Now watch The Secret of The Mimic being that he killed the real William Afton in 1983 and the Afton we thought we knew never existed. Or Afton came to possess The Mimic and used his own corpse as a people suit and that's why he's purple.
Edit: That might actually be an interesting AU.