I seal holes in plastic lures with bondo.
I drill the holes in the top of the lures, so the filler won't affect the movement of the ballast or rattles I add.
Then I spread some bondo evenly on the sticky side of blue painters tape, and put it over the hole, smoothing it down as much as I can while it's soft, but not going crazy.
With the bondo sticking to the tape's adhesive, I can keep the bait sitting upright, with the loose balls away from the bondo, until it sets.
Then I remove the tape, sand down the bondo until only the round plug in the hole is left, wipe it down with acetone to clean the plastic, and add a drop of crazy glue to the bondo to make it stronger, and help it really stick to the sides of the hole.
If I do it right, there's very little bondo exposed below the level of the bait's plastic body, but it doesn't seem to matter if there is a small bump inside, since it's on the top, away from the moving balls.
I've done dozens of baits using this method, and I haven't had a failure.
Another advantage to having the filler in the back/top is that the darker part of the paint scheme is usually on the back, and it hides the bondo.