Add new fragment inputs to `maxInterStageShaderVariables:at_over` test

[ErichDonGubler]

Add the following to fragment inputs that deduct from the I/O variable limit:

• primitive_index
• subgroup_invocation_id
• subgroup_size

I was originally hoping to handle this as part of #4538/#4539, but complications in the PR made me down-scope it.

Covers gpuweb/gpuweb#5403.