"In principle, could the time delay between the emission and absorption of a single photon in vacuum be measured?"

I'm sure I'm missing the point of your question here. I'm curious, could you please explain.

Are you simply talking about measuring the speed of light?

By measuring the time delay between emission and absorption of a photon over a known distance should give you the speed of light speed. Since you already know the distance and the speed of light in a vacuum is constant, this leaves you with an expected time of flight.