Your refer to the period when it was "extremely rare for a Consul to command more than two legions."
You correctly state that for a long period of time Rome only had two legion. However, during this period, each legion was commanded by a separate consul. (There were two consuls.) And, during this period, it was most exceptional for both legions to work together.
The whole idea between the two consuls and two legion arrangement was based on the notion that no single person should ever command the entire army, so as to avoid a coup. As a result, there was no provision for both legions to work together under a single command. Christian Meier wrote a great book where he takes some time to explain the Roman Constitution and gives great insights into it. I strongly recommend it.
Combining both legions, as in Cannae, was truly exceptional. Roman ways did not provide a command solution for such an exceptional circumstance. In fact the whole idea between the two legion and two consul arrangement was to prevent a single command. At Cannae the two consuls marched together alternated command of the entire army, one day each. A rather counterproductive solution, and clearly an exceptional arrangement under exceptional circumstances.
Furthermore, you state that "Polybius tells us... that six military tribunes were posted to each legion." Accordingly if you ever were to combine the two legions together, you would get 12 military tribunes for two legions. 6 +6 = 12.
In the very exceptional case where both consuls marched together in a combined army, at least one of the consuls would keep direct command of his legion while the other consul assumed command of the combined force. So only one legion, at most, was left without his consul commander. And, hence only in one legion needed to make special arrangements you cite. The other legion would retain its own consul plus its full staff of Military Tribunes.
The combined army would have 2 consuls and 12 Military Tribunes. One consul to exercise control of the entire army. One consul to command one Legion. 10 MT's would be available to assign 1 Military Tribune for each pair of cohorts. And you still have two Military Tribunes left. As per your suggestion, these two MTs could take operational command of the remaining Legion. Alternatively, one of them could take command of this remaining Legion, while the other MT took command of the cavalry.
Finally, we agree, if the consul (or legate) was missing, Romans most have provided a command solution where the military tribunes assumed temporary command in his absence. But this was a temporary solution in the absence of the consul (or legate). If the consul (or legate) was present, he was the commander of the legion.
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