Using MC 1.12 and Waystones version 4.0.5, for some reason, even though the config setting for waystones costing xp is set to false, The waystones are still costing me xp levels, no crash or other issues and mod is great, been using it for a long time now.

Thank you in advance.

The config option is called "Warp Stone Costs XP" - it only affects the Warp Stone, not Waystones. If you want to disable xp requirement for everything, set Blocks per XP Level to 0.