Yes, so much yes on the first part! Want to implement the simplest thing in UnityGLTF? You have to fork it, and force all your users to use your very special fork.

I assume you mean my 'nna' project with the second part? That serializes data into the node-names of the model's hierarchy. It is as stupid as it sounds, but it works reliably, and I don't need to modify any exporter/importer. The data is part of the file itself.

If you wanted to embed data into a format more legitimately, you would have to modify its exporter/importer, and the format would have to support extensions in the first place.