Pretty sure you are wrong. According to U.22 Kovacic's registration would be temporary transfered to Chelsea during the period of the loan

The Temporary Transfer of the registration of a Contract Player and any extension thereof shall be effected in accordance with the provisions of Rules V.6 to V.10.

Additionally, if I'm reading this correctly, it seems to specifically say that we need to follow rule v.6 and v.10, not v.7 which is the one you cited.

My understanding is that we have his registration until the end of the month and if we are buying him we're just extending it the same way we would do with a player signing a new contract.