Puckman and Pacman in MultiFE would simply just shown as they was their own game, something like this:
Pac-Man
  Pac-Man (Galaxian hardware)
  Pac-Man (Hearts)
  Pac-Man (Midway)
  Pac-Man (Midway, harder)
  Pac-Man (Midway, with speedup hack)
Piranha
  Piranha (hack)
  Piranha (older)
PuckMan
  Puckman (Falcom?)
  PuckMan (Japan set 1 with speedup hack)
  PuckMan (Japan set 1, Probably Bootleg)
  PuckMan (Japan set 2)
  PuckMan (Japan set 3)
It can been a problem in ROMLister too, since it want to remove dubles, unlike MultiFE who just want to shown them all clones into own "folder" (like the tree in MALA example).
Here I think you could add a default string filter which can been defined by the user, something like this, so some unwanted clones can been removed before trying to pick a game from the "list":
"harder)", "hack)", "hardware)"
it might take a while to pick and write a good search string to remove games that is not needed at all.