If glTF Transform (using Meshoptimizer internally for simplification, essentially the same as gltfpack in this regard) is not reducing the vertex/face count as far as you need or expect, then this might be a deeper question about the input geometry or parameters. In general, it should be possible to collapse a topologically-connected input geometry to nothing with the most aggressive settings.
Could you share an example of the geometry you’re having difficulty simplifying? There are some known limitations and workarounds possible.