Several possible reasons, depending on the model in question. Here are two.
1) Some of the earlier kits had extremely accurate bodies, because when they were the basis for promos, they were developed from OEM blueprints and had few measurement and scaling errors we often see today, or the creative "artistic" interpretations of proportions.
2) A significant expense incurred in tooling design is the layout of parts and runners, injection points, the need for sliding elements in some cases, and other esoteric things directly involved in the molding process. Scanning a known-good sprue eliminates a large part of this design and development labor.
We could hash out the relative benefits and drawbacks of doing things several ways, but we have to assume the tooling and design guys know what they're doing, and will make the rational tradeoffs between accuracy, cost, potential market size, etc.