"Does it matter how the ship is flagged?" - Probably not for large fleets, see [0] for examples of how this might be applied to the 2020 change.

Your ship may be registered to a tiny little island that won't enforce any regulation, but there's a limited number of markets to underwrite the insurance you need, and you'll want to dock at major sea ports.

[0] https://uk.reuters.com/article/us-shipping-fuel-sulphur/new-...