The fix is probably to call the same apply_settings() logic from script.on_configuration_changed.
Right now the saved setting still shows 1000, but the actual LuaForce bonuses stop applying after a mod config change. Reapplying these in on_configuration_changed should restore them:
character_build_distance_bonus
character_item_drop_distance_bonus
character_reach_distance_bonus
character_resource_reach_distance_bonus