I don't think the arrangement you describe is uncommon. For a gravity drain to work
the bottom of the holding tank has to be above the waterline, and most holding tanks
end up getting buried much deeper than that (amongst other things, it's nice to keep the weight of a full tank low in the boat).
Depending on the room available, a few tanks may have the pump connection on the bottom, but it is usually an internal stinger from the top. So, the only exit is by suction from the pump out connection on deck. That can be the marina pump out or your own on-board pump. Either way there will usually be a "heel" of liquid in the tank that cannot be removed. To get the tank as clean as possible you have to rinse with water
, pump, rinse, pump... Not ideal, but the way many installed tanks work