The reason companies like Matrix or Monolith or AlphaDream or Brownie Brown (now 1up) exist is because these are developers trying to be independent of Square Enix. Oddly, many of the "ex-Squaresoft" end up under Nintendo.
Also do you have a source on TOSE? TOSE is a big deal - nearly 1000 titles under their belt with few credits to match. They are programming and middleware kings and often nothing more.