What is the best way to semi-permanently seal and waterproof a pipe containing two cables?
fit a tee to the pipe so that each cable can be separately sealed,

Ideally use the parts designed to do this job, conduit and waterproof cable glands, not "pipe" and "stoppers"

fitting a downward facing tee part way along the conduit will prevent any drips that get through the seal from reaching the electrical box.