The load balancing is not critical as far as I know. The inertia /should/ cover it. Thermal issues should only mean don't overload any one winding past it's ratings.
But if you were going to do this a lot and were pushing full load on two windings (which is 2/3 of the total rated load of the generator!) with nothing on the third, I'd call Onan/Cummins (or whoever built the unit in question) and make sure they don't have any objections that I can't foresee.
The definitive answer is to "Read The (Friendly) Manual", but you already knew that... ;-)
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