You need a certain sales volume to justify the cost of development and tooling on a new product, and SFF is a niche that doesn't achieve high sales volume naturally. As a consequence, you need to do everything you can to maximize the market reach of a product, which means greater compatibility among other things. If someone doesn't buy your case because it won't fit the ATX PSU you already have, or the CPU cooler, or the GPU, then that's one lost sale that you could've had if it did.
This is also one reason the boutique cases are more expensive, on average: since the sales volume isn't there, high volume manufacturing techniques like die stamping don't make economic sense, and more expensive and labor intensive methods must be used instead.