Why would this cause any problem? When the boat is in the water, isn't that like having the hose in the bucket?
How does the water get into the cylinders from the cooling system?
It, or rather the antifreeze/fresh water mixture, will siphon back into the valve chambers if you crank without the engine catching (see above). The A4 can run "dry" for a couple of minutes from cold if you are just attempting to start it. You can even plan for this.
When you replace the impeller (and after four years on the hard, you WILL want to do this...and get a circ-clip pliers to make life easier), you will want to check for leakage at the pump body-to-block gasket, and you will need to find "pump grease", a waxy sort of hard grease like beeswax, to put in the pump shaft lube port (the little screw-on cap you periodically tighten). If you don't have this, a thick blob of lithium grease will do, but won't last as long.
When you fit the new impeller, grease that entire area with lithium grease as it will keep the new impeller nice and slippy for the short period you intend to run it dry, as it is the water itself that keeps the vanes supple.
Start the engine (you should already have put in new spark plugs, check the spark wires, checked the coil and distributor connections and made sure the batteries are serviced and charged and that you've got a new alt. belt on that is properly tensioned. You also better hope that the fuel system was COMPLETELY drained and the carb was fogged or otherwise cleaned and that the gas is completely fresh and the tank vent isn't a spider condo. But I digress.
Once the engine's running, in neutral, watch the gauges to see if the alt is charging and the oil (which should be fresh and "pre-cranked" by hand into the cylinders) is at 25-40 PSI. Watch the temp gauge. It can go from 100-150F without harm, but that could take five minutes in neutral, so you have plenty of time to drop a hose into a bucket once you've got it running. It helps to have a second person to handle the bucket to catch the old antifreeze, to read the gauges, and to stop or start the engine while you run this checklist (and it's only partial).
My point is that there are several ways in which an Atomic 4 won't start or will look like junk when it isn't...someone just forgot to do the right thing.