Compile a version of MESA without the extension. Or try writing a layer that hides it from applications.
#disable khrPresentWait.presentWait 2
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Here is a starter guide to writing Vulkan layers: https://renderdoc.org/vulkan-layer-guide.html
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Install the Vulkan headers such that CMake can find them, or manually point CMake at them. Nothing specific to Vulkan.