As it is now Atolls are spawning all over the globe.
Putting this aside for the time being, and making the assumption that most of these atolls are in fact isles, lets focus on the benefits.
Looking at 1 map and following the coastline I have the following types of terrain/features:
Terrain/Feature Output Tech required + extra step for output
Coast 1

Coast/Fish 2

[Sailing] + Work Boat
Coast/Pearls 1

+ 1

[Sailing] + Work Boat
Plains 1

+ 1

Plains/Wheat 2

+ 1

[Agriculture] + Worker improvement
Hills 2

Hills/Sheep 1

+ 2

[Animal Husbandry] + Worker improvement
+ on all Hills 1

[Mining] + Worker improvement
Jungle 2

Jungle/Bananas 3

[Calendar] + Worker improvement
Grassland 2

Grassland/Cattle 2

+ 1

[Animal Husbandry] + Worker improvement
Grassland/Forest 1

+ 1

Grassland/Forest/Deer 2

+ 1

[Trapping] + Worker improvement
+ on all Forests 1

[Constuction] + Worker improvement
Tundra 1

Tundra/Stone 1

+ 1

[Masonry] + Worker improvement
Add to that 'Luxury Resources' may also appear on tiles next to coast and you can then have 1

extra.
Now I haven't listed all the tiles generated on this one map but hopefully it provides enough background for my argument.
Atolls give 2

+ 1

straight away.
No need to research anything to unlock an improvement and no need to send a worker/work boat to improve it.
Clearly then that makes them more valuable then any other combination of terrain/feature/resource.
So if we want to provide a site with better tiles there are 2 ways to do it during the map generation process.
First method is as is done in this script, add atolls.
Second method, change that tile from a coast to a land tile with any of the available terrain/feature combos.
Because basically all that is happening now is the number of water/landmass tiles is changing.
In the actual generation of the map if a tile is currently a coast tile the tile next to it can either be:
Ocean = 1

Coast = 1

or any other land tile similar or compatible to surrounding land.
Making it Coast and then giving it an Atoll is just a convoluted way of making it more like a land tile.
Except it has the downfalls of being a water tile.
Maps currently have 1 tile 'peninsulas', or 'bumps' along the coast and it doesn't look odd.
That extra 1 tile gives benefits to any city near it and fits in perfectly with the overall feel.
Taking that 1 tile away, making it coast, and then placing an atoll to provide some value is an odd solution to a problem that doesn't really exist.
How far do we go? Down the track do we start saying tiles 'next to' atolls should have some extra benefit in the same way tiles next to freshwater sources do?