The way I see it, there are a lot of small design issues with having sea luxuries as regional monopolies:
- There is only one pantheon that super-charges them. So if two players get sea luxuries, one of them will get this pantheon and the other won't. It's a reward for rushing religion perhaps, but you don't get to know that it's a good idea until it's too late. There's not really play around it, and it's such a game changer, as your proposal is attempting to address as well.
- Having a sea monopoly means you'll settle coasts in an effort to secure them. Some civilizations really want this, others really don't. So it's very swingy how valuable that can be. On top of that, if you have a sea monopoly you'll stay away from your neighbors to a disproportionate degree, which disincentivizes interactions with the rest of the diplomatic and strategic game.
- Two sea luxury regions spawning adjacent to each other can result in a very un-luxurious inner land region, which leaves this barren kind of useless land. Probably the smallest issue of the list, but still something that happens.
- Sea monopolies setup pretty fast and have some fairly strong monopoly bonuses, especially early in the game. I think this contributes a lot to the pantheon feeling very strong as well.
So taken all together, I think the better design is to not have sea monopolies. You're right that it's a hammer, but I think it fixes several other things as well. It does mean the sea pantheon would also need further changes, which firmly puts it into counter-proposal territory.
But I also see your point, that my list might not be bad enough that it needs fixing. Sea monopolies makes for very unique games, which isn't to be ignored. It's not "balanced" but it is "special". And maybe that's more important.