And jobs are an opportunity cost - the people who would be working on this supervillain fantasy are not doing anything else. What could they, or would they be doing instead?
If building a submersible superyacht adds to the world, then well and good. Personally, I find the opportunity cost to humanity of doing so highly suspect. But I don't think I, or anyone, has a perfect picture of all the knock-on effects from particular money flows. (I think this is why a free market can have benefits.)
Jobs are not good because they are jobs, they are good because of what they accomplish, and should be measured by that yardstick.
It does still feel like a poor use of the world's finite resources, but I completely understand how it's not the individuals place to allocate resources effectively.