Your point about Lionel sending Lex to the crap factory is a case in point. If he knows for sure there's a "traveller" in Smallville, it seems like a dumb decision.
I'm thinking "Lineage" could give us adequate fanwank material for that. Lionel knew he burned his bridges with the Kents (well, Jonathan at least) with the blackmail to get his foothold in Smallville. He also strongly suspects Clark is the 'traveler' because of arranging his adoption (and the spaceship in the back of the pick-up), and clearly remembers the boy's affection for his son in that pick-up truck. Lionel's patient, remarkably adept at anticipating human behavior and manipulative. He sent Lex to Smallville to get an inroad to Clark believing they'd be drawn together - and he was right.