There is no specific program for adding metadata to tiles. Some of the required functionality for that does already exist in the 3d-tiles-tools. This is not exposed as an official/public functionality - so the implementation may change arbitrarily, at any point in time. But a very basic demo of the relevant classes that can be used to create glTF assets with the EXT_structural_metadata extension can be found in the ExtStructuralMetadataPropertyTable demo. If you have any feedback or ideas about how that should be made available, feel free to drip your ideas here or in an issue in the 3d-tiles-tools repo.