You can but why not do it by using the priming lever and saving the battery for other things? You will have to be sure the mechanical pump is not sitting on the cam lobe to ensure the lever gives full stroke!
As my tank is well below the engine Beta suppliedan electric pump. It's a solenoid operated thing and makes a clatter but works fine. I connected it to the key switch so operationis automatic. It makes filter bleeding very easy.
Your setup sounds exactly like mine. I have a Vega with the fuel tank in the encapsulated keel.
I fitted the electric pump immediately after the tank. This means that the filters are under an unknown positive pressure. The electric pump isn't protected by a filter.
I've only done 70 hrs with this set up and all OK so far but would be interested to hear of longer use.
My pump is also noisy - I blamed the fact that I had mounted it rigidly to an engine bearer - I keep meaning to remount it with some sort of noise insulation.