I'm sure they knew, and had a mitigation plan in place. Almost sounds like there weren't a lot of options.. "this is such a large project that there are hardly any locations where this work is finished."
And even if the municipality were to pay for it "Rotterdam has also been declared the maritime capital of Europe. Shipbuilding and activity within that sector are therefore an important pillar for the municipality." Seems like a fee they would be willing to pay to hold that title, or would be required for it. How is it any different than a state subsidizing a business district to generate jobs and taxes?
No, Bezos is paying for it.
Alternatively, it may have been a case of "if we get permission great, if we don't then we'll install the masts elsewhere for an extra several mil."
What's even more puzzling is that the problem is only with the masts, and it's apparently not possible to detach the masts and reattach them later? If I were Jeff Bezos, I would be worried about what this means for future repairs to the yacht...