A custom insole is only as good as the person who is making it. Is he/she making 10 insoles a day, a week, a month, a year? No matter which system he uses a good bootfitter should be able to craft a quality product that compensates for reasonable alignment and fit issues within the insole.
In most cases a flexible foot benefits more from a more rigid product. The foot requires support and the rigid materials aid in that. Products like Amfit and the Superfeet Kork products would fall into this catagory.
The more rigid foot typically benefits from a more cushioned product. The foot is structurally sound and doesn't require more rigid material to support it. The downside is but that rigidity means less shock absorbtion, hence the softer materials. By design DFP (Dynamic Foot Positioning), and most of the Conformable line fall into this catagory.
The Peterson and Instaprint are also quality systems when done right can produce a solid footbed.
Every system I have mentioned can produce a quality when in the proper hands.