Prior to bug 19974 a user could set an item to lost via additem.pl and the item would not be marked as returned and the patron would not be charged the replacement cost. The previous bug sought to standardize behavior between additem.pl and moredetail.pl, making both pages mark lost items and returned and charge the patron. Based on feedback about existing library workflows that relied upon the discrepancy between to two behaviors, the MarkLostItemsasReturned syspref was added to give libraries a choice of when and if an item would be marked as returned when set to lost. However, no such syspref was added to give the option to maintain the inconsistent legacy behavior in charging replacement costs when items are lost. This breaks existing workflows for libraries using lost status to handle Claims Returned items where the intent is to mark an item as lost but not charge the patron.
I can imagine a "Don't charge lost fee if checked out" checkbox next to the mark lost button on the item details view.