A very tough problem to solve: you organize by customer and you start to get requirements driven by particular customers, making your more of a custom dev shop that can't scale the business. You organize by engineering team and you become a project manager with less visibility into customer needs. You organize by Product, intersecting between projects and customers and you end-up with lots of ownership questions and gaming by PMs (strong PMs often will circumvent others to get satisfy their customer and/or project deadlines).
I've settled on the same conclusion as I've grown our team (and tried out all of these pivots along the way)... focus on the product and scaling the business out. Settle cross-ownership disputes by trying to clarify who makes the decision. Reflect regularly and adjust accordingly.