This issue has a different cause, please close it for now.

After some experimenting, I've found that plants can generate both before and after villages.

I made a datapack that shows this easily. Create a world with the datapack, and use the /locate village command.

You can see plants generating normally in the grass areas, which means they do generate after structures. You can also find plants on top of smooth sandstone.

Notice that plants never generate on the smooth sandstone in the rest of the world, so they can't naturally generate there after the structure. It means some plants generated first on grass and got their ground or part of them replaced by structures. This is basically what causes MC-140242.

In the lower grass area you can find plants that both generate before (and are thus cut) and after the structure (generating normally).

In the other image you can see this example with a support island. Villages have their own support islands so that they don't float, and it might be related to this problem.

I suspect that vegetation is generated for the island first, and then normally for the entire world.

It can be fixed by simply having all vegetation generate after structures. More information that can be found in MC-223305.