Nowadays, the alternator is often controlled by the engine management (which is essential for some batteries) and it won't produce any output at all unless the EMU is already working. Indeed, some (maybe even all) EMUs won't let EMU controlled alternators start generating output until they are sure the engine is started, to reduce the load on the engine whilst it starts and the starter is pulling the battery volts down, which would otherwise cause a heavy alternator load.
With a flat battery, it takes less than 5 minutes with a 4A charger to get enough into it to start the engine, providing the engine normally starts first time. One problem you might have is that many EMU's lose their learned memory of the optimum engine settings when they lose power, and that can mean that an engine that normally starts first time might not in this case as the EMU falls back to initial factory settings until it relearns the engine characteristics.