With the khronos_validation.gpuav_select_instrumented_shaders/VK_LAYER_GPUAV_SELECT_INSTRUMENTED_SHADERS feature, an application can control which shaders are instrumented and thus, will return GPU-AV errors.
With the feature enabled, all SPIR-V will not be modified by default.
Inside your VkShaderModuleCreateInfo or vkCreateShadersEXT pass in a VkValidationFeaturesEXT into the pNext with VK_VALIDATION_FEATURE_ENABLE_GPU_ASSISTED_EXT to have the shader instrumented.
// Example
VkValidationFeatureEnableEXT enabled[] = {VK_VALIDATION_FEATURE_ENABLE_GPU_ASSISTED_EXT};
VkValidationFeaturesEXT features = {};
features.enabledValidationFeatureCount = 1;
features.pEnabledValidationFeatures = enabled;
VkShaderModuleCreateInfo module_ci = {};
module_ci.pNext = &features;