Nah... Malindo is not really different from, say, Thai Lion Air (under Thai AOC) -- they're all part of the Lion group -- just like Tony's various AirAsia subsidiaries fly under different AOCs but are all part of the AirAsia group and all report to Tony.
In fact, Malindo was Lion's expansion into Malaysia to counter AirAsia's expansion into Indonesia. Tit-for-tat between the two groups.
Under the term's of Malindo's joint venture, Lion Air provides all aircraft and crew, while the Malaysian mostly-silent partner Nadi provide MRO services.
Malindo's CEO Chandran Ramamurthy was appointed by Lion Air's chairman Rusdi Kirana. He was Kirana's right-hand man in Jakarta.