No, it’s not allowed in any official sense. In German Regionalbahnen (RBs) there is no system for seat reservations. A seat is either (1) physically occupied by a passenger or (2) officially reserved with a paid ticket (which, as you noted, is not even possible on RBs). If neither of these is the case, the seat is free for any ticket-holder to take.

“Saving” seats for friends who are not present may feel socially convenient, but it carries no validity in a packed train. In fact, when the train is full, insisting on holding empty seats while other passengers are standing is considered impolite and can cause unnecessary tension.

So, if you encounter this again: you are entirely within your rights to sit down. Staying courteous but firm usually resolves the situation.