Is Having Multiple Charge Controllers on a single 48V System/Battery Bank a "Bad Idea"?
I was headed this way until about 2009. In the most modern and expensive setups you might have all the devices communicating and coordinating. In most, each one has its charging parameters that it's trying to meet, and the only communication is the voltage on the bank. 

With multiple, uncoordinated charge controllers you may exceed the optimum charging current, and you should expect to have disagreements among uncoordinated charge controllers (and a water turbine with no charge controller) as their charging set-points and algorithms are almost certainly different.

If you have the money to put into it, or you see it as saving money on the battery bank's lifetime, a set of networked, coordinated smart charge controllers would certainly work more optimally (and can all work at the same time) - but you should also realize that any system that won't leave you in the dark for large parts of the year is going to have some excess capacity when everything is going well, charging-wise. 

You can't simply add more battery without making it really hard to get it fully charged and equalized, and you can't reduce power sources without finding yourself in the dark after a few dry, cloudy, windless days. So sometimes, you are going to be dumping excess power. If you can do something useful with that power, great; (laundry is a good one, often) otherwise it's just part of the cost of having power more of the time. In the case of a fuel burning generator and a wind turbine, common sense would be to shut down the fuel-burner on a windy day.