There are definitely some features omitted from Apple's GPU, but fairly early in the reverse engineering process, Alyssa Rosenzweig provided several examples of hardware features present in Apple's GPU that are not exposed by Metal: https://rosenzweig.io/blog/asahi-gpu-part-4.html

Maybe, but we got here because I asked "is it possible that Apple doesn't want to support Vulkan (in software) because they don't want to support the features it needs (in hardware)."

If the reason they don't support the features Vulkan needs in hardware is because they don't want to support them in software, the logic gets a bit circular.

I'm interested in which came first, or if it's a little of both.

Vulkan very much is designed to give flexibility to hardware vendors. Where abstractions do paper over differences it's generally where it makes the abstraction cheap in runtime but you might take more code vs. less code but requiring a feature that would be otherwise optional (for example some of the complex pipeline manipulation Vs bindless)

Perhaps, but also geometry shaders are generally losing popularity and on their way out. Per google ai search result (for what it is worth):

Geometry shaders are generally considered less necessary in modern graphics pipelines due to the rise of more flexible and efficient alternatives like mesh shaders which can perform similar geometry manipulation tasks with often better performance and more streamlined workflows