Yup pretty much impossible to drain all the water out of the drain hole, not sure why you need to flush out the inside of the yak? You wouldn't want the drain hole on the base of the keel or anywhere else below the water line for that matter as failure to do the bung up properly could have disasterous consequences.
I agree with ganiom about leaving the hatches open, dries out residual moisture nicely, also mitigates against expansion and contraction of air inside the yak due to temperature changes when it is stored.
However I am sure the Hobie engineers could come up with a better place to put the bung.
on occasion i like to flush out the inside of my hull because i fish saltwater. my battery is also located in the hull. so i try to get as much salt out as possible, even if it has no adverse effects on my electronics (doubt it), call it OCD then.