Squid seem to be very intelligent, like octopi. It was probably tired and needed a rest. So hitch a ride via suction cups..........
Going back to a part of the article:
Shigeo was sailing through a very fertile piece of ocean, known for its population of sperm whales. Sperm whales eat giant squid. And often have scars from the suckers.
Think of it as a Crip needing to get across Blood gang territory and hitching a ride by hiding under a passing mobile home till he got to somewhere safe.
Smart squid.
The other alternative is to think of it as a ninja squid, using this boat to sneak into hostile territory undetected...
Now there's an image! I wonder if the squid had a suicide vest strapped to his body?