There's no real reason for a customer to care about these trade offs. They want to get work done, nor worry about the business model behind one of their tools.
That's looking at the problem backwards: if you have one customer who has a bunch of customization requests you need to weigh their business against what other work you could be doing with the same development time. It's not a win if you keep one customer but lose others to a competitor whose product is easier to use or cheaper to develop, especially since I've probably seen at least a 1:10 ratio for arcane features and customizations which a customer swears up and down are mission critical to things which actually are — usually it's more like one guy doesn't want to consider changing the way he works in the slightest until forced.