Doesn't sound like a good arrangement.. I have already identified the
potential problems.

Is there some reason that you can't use a water-lift chamber (muffler) to
get the engine end of the system higher than the waterline. Thus the pipe
would run down hill from the outlet of the waterlift.

A water-lift is suppose to have enough cubic volume to contain any and all
water that may remain and run back into the chamber. When the engine is
started the next time, there will be enough pressure to "lift" that
residual/run-back water up and out.

One potential problem with a water lift, is over cranking an engine. While
cranking the stubborn engine, the water pump will be filling the water-lift
to a point it may run back into the engine exhaust manifold.

BTW. I had a 59 Chris Craft with twin 289s. The exhaust system had no water
lift or a muffler.. The exhaust elbow was above the waterline (transom
discharge), however, like yours, the pipe was low near the engine and the
exhaust pressure pushed the residual water "up" the pipe to the transom
discharge. At normal draft, at rest, the transom exhaust was a couple inches
above the waterline. I had exhaust flapper the helped keep the pipe from
filling with water from any following sea or chop when the engines were
stopped.

--
My opinion and experience. FWIW

Steve
s/v Good Intentions