Okay. Reading over the previous discussions, I've decided to take a wild leap concering the Thoth term on 'We're Everywhere!', mostly based on circumstantial evidence, and making a number of assumptions.
Now Thoth was a S'pht AI created to preserve balance on the planet, but if the clans were in near-constant warring strife, none of these would have created a device that would keep themselves from gaining an advantage over the others. Thoth must have been made by some outside power, probably Yrro himself. Thoth even asks on a different terminal "Has(is?) jjaro come?" Which would indicate that he would respond to Yrro, any other of the Jjaro, or their creations.
Now. We know that the Jjaro had superb cybernatic technologies that could go so far as to even grant sentience to other species. These devices were used to create the S'pht, and attatching one to the Drinnol caused a massive slave rebellion. Going back to the old text from the Infinity end screen "A long-dead man built with machines his makers didn't understand", we can make an inference that the player may have been built with Jjaro cybernatic technology. They certainly knew of the Sol system, and may have left something behind.
So, maybe the Thoth term is responding to the detection of Jjaro cybernetics in the player, giving the proper pre-recorded response to such parameters?