I am not completely sure what you mean. But the PGN standard doesn't forbid any sequence of legal moves to be included as variation. So if GUIs do not support that, they are simply not PGN compliant, and should be fixed.
I don't understand the remark that "users do not want that". If they don't want to step through an included variation they can simply refrain from doing it. Annotated PVs being present as recursive variations doesn't clutter up the game text any more than those being present inside comments. Code that allows people to step through variations would not in itself care whether these variations were (partial) duplicats or not; it would require dedicated code to break this functionality and make the software PGN non-compliant.