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Looking at Vulkan Samples and other Vulkan materials even on mobile it seems that the right way to manage command pools in a transient way as they are used by wgpu should be enabling the right flag and resetting it without any flags.
Vulkan Samples:
https://github.com/KhronosGroup/Vulkan-Samples/blob/master/framework/core/command_pool.cpp
Arm Mobile developer:
https://arm-software.github.io/vulkan_best_practice_for_mobile_developers/samples/performance/command_buffer_usage/command_buffer_usage_tutorial.html
In my local profilings in my proto engine we're passing from around 9ms to around 800μs (more than 10x speedup)
No warning on leaks from validation layers is appearing in RenderDoc on my side too.