The problem for Rommel was getting the supplies ashore and to the front, not across the Mediterranian. From 6/40 through 4/43 only 8% of the men and equipment sent to North Africa was lost and, only 16.3% of the supplies. At the time of Alamein Rommel was receiving (after losses) an average of 56,209 tons of supplies a month (yes, loss rates during this period ran higher at 35.5% but the amount being received was still good as shown above). The problem was that about 60% of the POL products delivered went into getting the rest of the supplies to the front. It also meant that over half the trucks in N. Africa that the Germans possessed did nothing but suttle supplies to the front.
Had the Germans had a rail line across Libya available this would have freed thousands of rear area troops to the front along with vehicles and, would have alleviated the fuel shortage Rommel faced.