I'm slightly confused, if the owner can't afford to deal with the costs, they obviously dont have the financial ability to penalize the individual NOT to abandon ship.

That level of cognitive disconnect surely can't be held up as valid in any legal system that has greater cognitive ability to do 'connect the dots drawings'.

I would imagine it is illegal to abandon a ship in port

Illegal for whom? Surely it's illegal for the owner, or perhaps the captain at most, but not the crew?

There's a couple of reasons why the crew and officers don't just leave. One is that their employment record will show that they left their ship while their contract was still in force, which given that jobs in the industry are highly desirable will make them unemployable.

And the other is that the port authority wants the ship gone, and not vandalized or becoming a hazard to navigation. So they will require someone to stay on board to maintain it and keep it secure. Which can include getting Immigration to forbid the crew entrance to the country. While they are in port, it's much like being in the secure area of an airport - they're in a gray area and aren't actually in any country. So when that happens, it is illegal for them to leave it.

That story is probably due to coronavirus travel restrictions, given it is from last May.