The trademarking of the body design and the design's names are two completely different issues.
FMIC lost the patent application for the body design a few years because they had waited too long to file the patent for the design, after other manufacturers, that made Stratocaster-shaped bodies made their case to the US Patent Office as they themselves had been using the design to build their own. Please note that FMIC does own the patents to the headstock designs, which is why these other manufacturers do not use the same headstock design when making these similarly-shaped bodies.
FMIC does, however, own the rights for the names of Telecaster and Stratocaster, as well as the associated short forms. If any other manufacturer were to call their designs by the names Stratocaster, you can be sure that FMIC would file a copyright claim against them. This is why no company, not even G&L, use the names of Telecaster and Stratocaster on their guitars. The patents are held by the company, so when Leo sold the company to CBS, the rights did not follow him. This applies to other non-musical related products as well.
Warmoth has a licensing agreement with FMIC that allows to use thier various copyrights, like names and headstock designs.