You can replace the default loot tables by adding the files in

world/data/loot_tables/minecraft/

but you can't replace the structures by adding the files in

world/structures/
world/structures/minecraft/
world/data/structures/
world/data/structures/minecraft/

Steps to reproduce:

1. Download the base_floor.nbt attached.
2. Put the file in

   world/structures/endcity/
   world/structures/minecraft/endcity/
   world/data/structures/endcity/
   world/data/structures/minecraft/endcity/

3. Open the game now.
4. Test by loading the structure using a structure block.
5. See a bunch of pink wool.
6. Search for a natural end city that has not been generated before.
7. See that the base floor is still the normal structure.

Note: the attached file is even the same dimensions as the default file.