(maint) - replace matrix input with flags

[jordanbreen28]

Summary

This PR removes the no longer needed matrix input, and replaces it with a flag input. We can now force matrix_from_metadata_v2 to generate a matrix using only gcp vms, so the original reason for adding the matrix input is no longer relevant.

Checklist

• [ ] 🟢 Spec tests.
• [ ] 🟢 Acceptance tests.
• [x] Manually verified.