That is pretty much a common situation. If you are camped in one spot, you don't tend to pull air into the pump until you are nearing the end of your water supply. But if you travel with a low tank, you will definitely pull air into the pump if you are much below half full.
If you search this Alpine Coach forum you will find a couple of solutions. Some have had a new fitting put onto the bottom of the tank so that they can get all the water. Some clever person put a Tee in the fresh water drain with a 1/2 fitting on the side, and used that for the pump connection point. Seems like a good idea to me.
I have a SeeLevel gauge with more resolution on the water level, and it showed me I tend to run out at 11 gallons of water. I have not tried to find a way to get that final portion of water. I am happy with the 90 gallons I can get as is. But if you dry camp you will want to get that final portion.
'04 Alpine Coach 36' MDDS