In general I think there is a discount to working at a non-profit. I'd expect a salary bump if I went back to industry. That said, I think it is not uncommon. Non-profits span a wide range of organizations. There are well-funded non-profits like the Gates Foundation, Simons Foundation or the Chan Zuckerberg Initiative, medical research institutes and research hospitals, health insurers, and leading museums. Non-profits report salaries of officers, highly paid and key employees. Have a look at ProPublica's Nonprofit Explorer [0]. Look for IRS Form 990. It's pretty interesting. As tsunamifury says, if you can demonstrate strategic value to the organization you will be in a strong negotiating position.
[0] https://projects.propublica.org/nonprofits/