Ben, it might help to clean up your nomenclature a bit. A point-to-point generally refers to a pod-and-rail machine used in conjunction with a beam saw where the part blanks are cut and then machined on the p-t-p. Most nested base machining takes place on a flat-bed router.
Both approaches can be equally effective. With a router, you generally have just the one machine (of course you can have multiple machines), the one footprint, and less handling of the parts between machines. With a saw and p-t-p, you need space for two large machines as well as room for loading materials, etc.
With a saw, you can cut larger volumes of parts by cutting stacks of material and you're not spending time at the CNC machine cutting the perimeter. If you do a large volume of like parts (catalog-based), the saw and p-t-p might be the way to go. If you're doing a lot of customization, it's harder to take advantage of the saw's efficiency, in which case nesting might suit better.
A lot of the software packages available focus on nesting and some don't address saw and p-t-p at all. When using a saw, especially if you cut a lot of material, simpler patterns and fewer saw cycles should be factored in along with material yield. As with anything else, some software does it better than others.
In the shameless plug department, CADCode's software covers both forms of manufacturing and some shops do both.