If you get the Y-Wing then you could run two Y-Wings in either Scum or Rebel.
If you get the HWK you'll only be able to run Y-Wing/HWK in Scum but only use the HWK in Rebel squadrons because you have no rebel pilots for your MW Y-Wing.
Ehh, depends how people feel about proxies. A Thug and a Gold Squadron pilot chit are wholly identical but for the name and the color of the fire arc.
And if you want a pair of Golds you end up needing the extra chits either way, so the 'two Y-wings' approach has less flexibility than at first glance.
If you don't care about proxies then it really shouldn't matter what you get beause you can just call it what ever you like.
If you can tell my feeling about proxies is DON'T. If you're going to start doing that then why stop at upgrade cards or even cardboard which is what is being suggested there?