As others have stated the reason is to ease the configuration of each client. Although when I started I used 1 folder and it was fine. Now with ISBoxer I run virtual configs for each and it works great.

Off topic but in response...

I use ISBoxer and have found it to be quite nice for boxing, with a little work it really makes life easier. Not sure what's so scary about it as using it as-is doesn't promote or enable anything questionable. Could you? I am sure with some work you could, but saying that you could do that without it as well.

There is room for both hardware and software boxers, I don't think we need to be so opinionated on one or the other. Grow the field, support one another and have fun.