vk_shader_decompiler: Fix vertex id and instance id

Vulkan's VertexIndex and InstanceIndex don't match with hardware. This
is because Nvidia implements gl_VertexID and gl_InstanceID. The math
that relates these is:

gl_VertexIndex = gl_BaseVertex + gl_VertexID
gl_InstanceIndex = gl_InstanceIndex + gl_InstanceID

To emulate it using what Vulkan's SPIR-V offers (the *Index variants)
this commit substracts gl_Base* from gl_*Index to obtain the OpenGL and
hardware's equivalent.