Restore the default pipeline layout creation flag

Restore the default pipeline layout creation flag

Setting the VK_PIPELINE_LAYOUT_CREATE_INDEPENDENT_SETS_BIT_EXT flag
in the core framework makePipelineLayout() function means that all
tests, even tests that aren't testing VK_EXT_graphics_pipeline_library,
are creating pipeline layouts optimized for independent
partial pipelines.

This flag should only be set when actually testing that feature
since it can be less optimal than the regular pipeline layout,
and is not the default all applications currently use.

This CL restores the default flag and updates the tests that
need it to override the default flag.

Affects:

dEQP-VK.*
dEQP-VK.pipeline.pipeline_library.graphics_library.*

Components: Vulkan

VK-GL-CTS issue: 3609

Change-Id: Iabc8643707f03878426c9bbe87bc0c9ee856bfb3