By the power of truth, I, while living, have conquered the universe.
(Credit to Roberto)
In a physical sense, I think it's possible that the Timeless One was never physically present, but rather using the Gravemind as a conduit for his mouth (like the Mouth of Sauron from LOTR). The giant venus fly trap we see in Halo 2 got completely obliterated twice, once in the Forerunner era and once in the contemporary era, yet the Gravemind still survived. And before any of you say the Gravemind in Halo 2/3 is not the same as the one from the Forerunner-Flood war, it is.
Three things: Firstly, the Proto-Graveminds are a physical entity that requires much more substantial amounts of biomass to be created then what was present at 05 (as I covered). Second, when the Proto-GM dies, everything in the local Flood hive else dies, and it can be killed by conventional means, which the real Gravemind cannot. Third, he speaks as if he's extremely old and has experienced all things the Flood did 100,000 years ago and even before then - how can he know what happened if he was formed in 200 years after the Flood broke out on Installation 05?
The venus flytrap is a mouth organ, for him to speak verbally to the Chief and Arbiter. That was "destroyed" in Halo 3 during the High Charity explosion, yet GM survived again and begun rebuilding itself on the Ring. Installation 05, I believe was also glassed to kill off the Flood. He survived that too. And, according to him at the end of Halo 3, he survived the Halo detonation as well.
All of this indicates the Gravemind might not truly have ever been present, and that he was somewhere else, a long way from possibly even the galaxy, projecting his mind into the Flood.
Its this case with the Bestiarum that originally lead me to believe that the Gravemind was not actually present at Installation 05, High Charity or 04b, but rather the Prisoner was somehow psychically projecting his consciousness, or a part of it as the GM can apparently do so with individual Flood, to converse with Cortana.
This is also supported by the fact that the Flood are a hive mind and seem to have some kind of neural/telepathic connection between one-another (evidenced through the GM speaking through a Tank Form in Halo 3).