Since they're recasting Batman it's a good bet that they won't use anything from Smallville or any other incarnation of Batman that we've seen.
was an incarnation of Batman?
And many characters created for adaptations of comics -- from Jimmy Olsen and Perry White to Harley Quinn and Livewire to X-23 and Agent Coulson -- have been adopted by the comics and by other adaptations. Chloe Sullivan from Smallville
has been added to the DCAU at least briefly. So there's no reason a Superman movie couldn't use a version of Lionel Luthor if they wanted. They won't be here, but there's no reason they couldn't.