The reason Tobruk and Benghazi were not used by the Italians, was because the route to Tripoli was much safer.
It doesn't matter if Tobruk and Benghazi have a smaller capacity than Tripoli; they still could have been used. Just send the heavy equipment (tanks, aircraft, etc...) through Tripoli, and the supplies Rommel needs immediately (oil, food, water, spare parts, etc...) through Benghazi and Tobruk.
One of the reasons Rommels supply situation was as bad as it was, was because the Italians would refuse to use any other port but Tripoli. They actually did supply Rommel a lot better than you would think (still, not enough of course), but since the RAF had air supremacy, most of the supplies got destroyed by British interdiction sorties.
Source please. I'm sumarising "Supplying War: Logistics from Wallenstein to Patton" by Martin van Creveld where IIRC he gives the exact capacity of all the ports along the N. African coast and demonstrates, to my satisfaction at least that, they were incapable of supporting any more forces than they did (and were in fact barely capable of supporting those).