Indomitable could physically host the command staff, but placing the aggressive destroyer officer Tom Phillips aboard the carrier could interfere with carrier command. HMS Renown offers another solution: she completed refit in November 1941, could exceed 30 knots, and carried modern radar and flagship systems. If Prince of Wales were disabled before deployment, Renown was the other available fast capital ship Britain might send east. A core of Renown, Repulse, and Indomitable would give Force Z three ships capable of more than 30 knots. Adding Renown goes beyond the strict ship swap, so this three-ship core is a plausible extension rather than the baseline scenario.
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Renown could supply the modern flagship Force Z lacked
Using Indomitable as flagship might disrupt carrier command, while modernized Renown could lead a fast three-ship core if Britain accepted an extra change beyond the strict swap.