OK, that makes sense; thanks for the extra information. I think this change happened because we used to map shader graphs by name (which would be the same for the shader graphs in the asset bundles), but switched to mapping them by instance ID (in part because names aren’t guaranteed to be unique).
Although it’s not the same as full support for shader graphs in asset bundles, I think we can put a fix for this issue in a subsequent release: we will fall back to mapping shader graphs by name as we do for built-in shaders if there’s no match by instance ID, and include all the shader graph MaterialX exports in the project in the build (mapped by name). That way, as long as your shader graphs have unique names and are in the base build, they will be loaded correctly when used in asset bundles (though the actual MaterialX file still won’t be loaded from the asset bundle, so you still can’t use shader graphs that weren’t included in the base build).
Sorry we broke this workaround! Hopefully we can get this fix into the next bugfix release and that will work for you.