From what I've gathered, because Toyota wants to keep the FR-S as their flagship Scion model, they're refusing to do anything extra with it. Outside of the U.S. they're all for whatever is done to the GT-86. The FR-S, however, is meant to be "cheap". If they finally killed off Scion and kept the FR-S, but released it as the GT-86, things might venture towards factory-released turbocharge.
People are forgetting that these cars were built to be AFFORDABLE RWD sports cars. Slapping a turbo on it misses the point entirely.