Because GT scaling is ridiculous.
Goku stated that 1st form Rildo was "even MORE powerful than Majin Boo", and Goku was stalemating him in his BASE state. From this alone we can infer that base GT Goku ~ SSJ3 Z Goku. When GT Goku then went SSJ1, Rildo stated that his power had increased "A HUNDRED FOLD." ie. SSJ1 GT Goku (100x) > base GT Goku ~ 1st form Rildo > Majin Boo ~ SSJ3 Z Goku.
The difference between Janemba and SSJ3 Goku was not even remotely close to 100x -- more like 2-4x, I'd wager. So as mentioned, SSJ1 GT Goku would utterly shitstomp Janemba... Which means almost any version of Baby is extreme overkill.