I forgot one detail: your ISP could pay a different tier-1 ISP, as they all interconnect. Nonetheless, your ISP pays top rates for that traffic - tier-1 routes are usually last-resort routes.
Obviously if the ISP is buying transit from HE, they'd have to pay for it, but it'd be surprising if HE was strongarming their customers by adding a clause that's like "oh also, if any of your customers use our ipv6 tunnel, we'll charge you $x/user/month" or whatever.