If you're a large enterprise, paying an extra $20/month could definitely be worth not having the pain & cost of having your employees having to manage paying an extra bill each month.
Pricing for the marketplace was completely left up to the discretion of the integrators. There's a number of integrations (ZenHub included) that are the same price whether you buy through the marketplace or through company websites :)
If you see it that way, yes. But getting people to sign up on your website without the 25% cut is also not for free, think about costly advertising and so on. This is probably what Github and other marketplaces bet on. You always pay for any channel, whether it's direct cuts or upfront costs to get a customer.