Comment by jacquesm

The fillet problem is not a problem. It is a problem if you try to apply fillets after you have created something complex. But if you generate it out of variations on the primitives that already have filets it gets much easier to keep control over the resulting shape. What OpenSCAD makes next to impossible is to first combine a bunch of primitives and then to do one more operation on the resultant shape. That's really fighting the tool. But if instead you define a layer just above your primitives that already have the edges the way you want them to be then you can combine them and the filets will stay where they were on the primitives. The problem that remains is to blend them if you need to, I've found a really simple trick for that: define spheres with the fillet radius and create hulls over sets of these. That allows you to fill in the gaps if there are any.