I think Gen did catch at least a little bit of Amos pre-their first meeting since I remember a tag in which he accused Amos of snivelling and crying and Amos didn't deny it... so he could've caught a stray empathic feeling if he'd been close enough at some point he just has no idea how to discern but this could be the start of figuring that out, with new bonus empathetic flickers...

God I'd LOVE for Amos to be the one to infect him though, please... Especially since there really won't be much, if any, change in his demeanour so it'd be really easy to catch him unawares about this. We can use that to facilitate some daydream glimpses to force them to confront each other's Mess down the line! Especially especially since afterwards Amos will be absolutely horrified at himself that he hurt Gen in all of this.