how could they legally patent the use of V in their combo patent without infringing the owner rights of Amarin? How could FDA approve such a cohort when found efficacious in the trial? How could GILD ensure they get a constant supply of V if they don't have an agreement with Amarin?
Patents grant applicants with the right to EXCLUDE, not a right to MAKE. You could submit a patent today using Vascepa, that if approved, would prevent Amarin from manufacturing your patented product. It's a strategy commonly employed by patent trolls. Of course, you would need Amarin's permission (usually through a licensing agreement) to use Vascepa to make your patented product.
As for a supply of Vascepa, they probably source it from a wholesaler like any other pharmacy, not necessarily through a partnership with Amarin.