Some transformations missing after transforming gltf file

[benthillerkus]

Using this viewer: https://gltf-viewer.donmccurdy.com/

Here's both a transformed and the original GLTF. With the transformed GLTF the window shutters are misplaced.
venice-transformed.zip

[clicktodev]

could be related to #235

[donmccurdy]

I think this issue is unrelated to removing UVs and normals: upstream issue in donmccurdy/glTF-Transform#1505 with details.

[donmccurdy]

To be fixed upstream by donmccurdy/glTF-Transform#1507. The cause of the bug was that glTF Transform's instance() function did not correctly handle files that already used glTF's GPU instancing extension, EXT_mesh_gpu_instancing.