There isn't anything SE can do, Level 3 is nothing to do with them, nor is Comcast anything to do with them either.

It's your ISP (Comcast in this case) that decides that your route to the Square Enix servers goes through Level 3 so the only way to resolve this is either:

1) Convince Comcast to route you via another method that doesn't use Level 3.
2) Use a different Internet provider that won't route you via Levle 3 (which I appreciate might not be an option)
3) Use a VPN service such as WTFast to tunnel your traffic and try to route you round Level 3 indirectly.

The big SE thread on this I think was partially to show SE was aware of this and so they can contact the ISPs in question... but other than that, it's out of their control. They don't dictate how your ISP manages your traffic and I can't seeing them wanting to pay Comcast to route traffic other ways because likely a lot of ISPs would suddenly start routing through Level 3 and want payment as well.