I have the slightly bigger cousin of your Otter; a 16 foot NRS Expedition. I know exactly what you’re talking about. The drain holes are way too far away from the bow and stern handles to reach from the water with the raft upside down.
I drilled holes in the seam between the floor and the tubes closer to the bow and the stern to add handles made of webbing.
Here’s some pictures of the process. I realize I forgot to take a picture of the final result from the outside, but there is a shot from the inside.
* Hat tip to Steve for mentioning this solution on an episode of gear garage.