Fix physical_device_groups custom instance usage

Fix physical_device_groups custom instance usage

The test is using a custom instance but misusing the default instance in
some API calls and expecting some consistency in the results.

In addition, the custom instance was not correctly collecting validation
error messages and some VkPhysicalDeviceGroupProperties structures were
not setting the sType as expected.

Affects:
dEQP-VK.info.physical_device_groups

Components: Vulkan
VK-GL-CTS issue: 3876

Change-Id: I3900723034bddb2dee0aaaab549cc6d362b1339e