Why would a guy facing federal charges be locked up in county jail?

He said the federal government was paying the jail to keep him. To me that implies that it's not a federal jail. If I remember correctly, I have visited individuals held on federal charges in a county institution.

Because there are no federal jails, or at least very few. So local/state agencies hold them until and throughout trial.

He wouldn't, unless they're pulling a "Guantanamo" on his ass.