Texture sets should only be checked for name (seeTextureSetMap)
Test custom configs extensively, make sure they are not overwritten (Golrith's issue)

Sounds like a great solution. Probably a fair bit of coding to change this, which is very much appreciated.

Golrith proposes:
"
Perhaps go the EnderIO route with the json files (especially the biome allocations file).

It has 2 jsons. One of defaults which the mod will update as required, and then a user overrides file, which the mod never touches.

It loads the defaults, then loads the overrides.
"

This is basically superseded by my current efforts to replace Tile / TextureSet / Texture with resource packs.