There are a number of reasons, first of all the alternator needs some power to it otherwise it won't produce any power itself, secondly a flat battery often won't actually take a charge, especially if the plates have been knackered.
Trying to charge a totally flat battery can wipe out the alternator as well, often the relays can get burnt out and you then have not only a flat battery, but a stuffed alternator also.
Basically if you need to hand swing a prop, have a think about why, if the battery is just low due to lack of use and it's a cold day, then hand swining may be an idea, BUT if the battery is actually dead, then at least try and recharge it with a trickle charger before going flying. If it is toast, then replace it, don't muck about with hand swinging just to get in the air.
This is especially true of turbine a/c that use battery starts. The lower the inital voltage, the higher the chances of a hot start and all the associated (expensive) problems. I've seen a couple of people damage £50k turbine sections because they've been too tight to put in a new £400 battery. Very stupid!
Make sure you always have a good battery, don't try to 'get away' with a duff one, it's a false economy.