The agreement between Hyperion and Individual only currently covers the Kickstart and not the rest of the OS. It's also unclear if that agreement would cover A1200 reloaded since the wording in the press release says "processor accelerators for Amiga 500, Amiga 1000, Amiga 2000 and Amiga 2500."
They need a different agreement for A1200R and that could come down to who offers the best terms and flexibility.
The only reason I mentioned it was because the agreement was made some number of years ago and neither Amiga Inc or Cloanto have taken issue with it and it pre-dates the deal for Cloanto to distribute 4.1FE Classic by almost 3 years.