The Founder likely knows who (/what) Orion is.
He's startled when he sees Orion in Eternum the first time.
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And then at Warthogs using the device on yourself shows a render that looks like kid Orion and the Founder
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Who knows what the backstory is. Maybe the Founder used Orion to create the first neural implant, maybe he was part of some type of experiment, whatever it is them sharing past history does remove some options.
What I find interesting though is the fact that he's surprised to see Orion. I mean, playing Eternum isn't anything out of the ordinary. His reaction tells me he thought Orion was dead or something.