Actually there is no evidence that the Germans could have advanced rapidly enough to seize functioning ports from the British. The British had planned for such possibilities and would have left very little in terms of functioning port facilities behind them. Not to mention that there were no ports of any significance west of Alexandria until you reached Tobruk(in Libya), which is not a short trip.
A German motorized division's supply needs were substantially greater than two Italian infantry divisions and, again, supply needs were already maxing out the port facilities in Libya. Likewise this massive increase in Luftwaffe involvment also requires fuel supplies being available on a much larger scale.
Bardia and Mersah Matruh could be used; hell the British staged a lot of supplies out of Mersah Matruh
The Germans seized ports from British control several times during the african campaign; airfields too for that matter; Bengahzi twice, Tobruk and Mersah... the problem was the ports took heavy losses from air strikes, and the Italian navy feared challanging the RN by sending the ships to the more forward ports; if you install a larger LW presence, it reduces those two factors, allowing the axis to take more advantage of the infrastructure they capture
Also, once the Germans are far enough forward, the RN leaves the area which conceeds a safer supply zone to north african ports; when Rommel reached Alemein, the RN ships in Alexandria were in range of stukas with fighter escort, making their position a dangerous one
The Italian line infantry divisions in Africa had enough trucks to theoretically lift half their men; and given that german motorized infantry divisions were fairly small; a strait 2 to 1 tradeoff would be supply net neutral
I don't disagree that Tripoli, and sometimes Bengahzi were loaded to the max; hence Tobruk and other forward ports need to be used to reduce congestion. The LW wouldn't have to base all of it's increased efforts in africa itself... ground support forces could be applied at the historical level, whilst the additional assets are used to supress Malta and Alexandria from the mainland and to fly top cover based on the mainland