This is the reason why Chuck Cunningham blipped out of existence in the Happy Days universe.
Cupcake is a - say it with me now! - Time Lord.
- Look at the controls for Cupcake's time machine - set in the middle of a room with big circles on the walls, with six sides full of unlabeled dials and switches. That is clearly a TARDIS control panel. (Of course, out-of-universe HB wanted to do an animated Doctor Who, she's clearly a holdover)
- Even weirder she may not be the first one in Hanna-Barbera, The The Super Globetrotters fought a guy who directly called himself The Time Lord, several years earlier.
- While the Doctor Who story is itself just an urban legend, it is very likely both the design of Cupcake's ship and that Super Globetrotters villain were intended as just plain old shout outs to one of the then time period's biggest television successes, and not so much being left overs from an animated DW series.