1. The single pass prefix sum the author implements is not legal Vulkan code. The algorithm requires spinning on conditions to be satisfied by concurrently running threads. This is allowed to deadlock in Vulkan and is mentioned explicitly in the "Limited Forward Progress Guarantees" section of the Vulkan Memory Model blog post linked to by the author. The only GPUs on which is it technically safe to run this algorithm are the Volta and newer NVIDIA architectures.
2. The mask argument of the CUDA shuffle intrinsics is there, not because it is a more powerful abstraction, but because compiler technology of today is unable to prevent illegal code motion of shuffle intrinsics. There are threads on the LLVM mailing list that discuss this in some detail.
3. I am happy to see this topic written about. Portability of compute algorithms and where APIs differ or lack is not well understood and CUDA tends to dominate the discussions. Regarding subgroup portability - I do wonder if asking developers to write their code for specific subgroup sizes and allowing them to request subgroup sizes is the correct long term abstraction. In Metal you can get a long way writing code that uses subgroup ('simdgroup' in Metal speak) functionality without actually making any assumptions about the subgroup size. It is a balance - there will always be performance to be had if you hard code such assumptions, but the more we can close the gap, the less it makes sense to do so.