I have a Checkpoint but do not ride in the rain, because we get very little. Closest I can come is I've washed the bike a few times, but I've never noticed water coming out of the chain stay. Not saying it doesn't but after washing I'll pull the bike up on the rear wheel and bounce it a few times to shake water out that doesn't just drain off in the normal upright position.

The down tube storage hatch doesn't have a seal, so that seem possible. If you really want to get to the bottom of it, stuff some paper towel or similar under the hatch. Run a hose over a bit, and see how wet the paper towel gets. Then of course, remove the paper towel and retest and see if you can get enough water inside that it finds it's way to the chain stay.

Of course there are other places water could get in such as the top of the seat post, at the seat tube clamp. Cable entries near the head tube. That type of thing. But unless you're riding in a deluge, it seems unllikely very much would get in.

The one good thing, if you're finding water draining out, you know it has in fact drained out and isn't sitting somewhere else.