It is my understanding that lower aH batteries (in general, not Bauer specific) cannot output as much current as high aH batteries, so higher amp draw tools like saws need the larger capacity batteries. This all depends on what cells the battery uses, amongst other things, and I'm not sure there is a clean dividing line of aH ratings so I would probably just follow Bauer's guidance. Cordless manufacturers use a lot of meaningless marketing terms like "50% more power" to describe their batteries rather than rating them in terms of max current draw, but you can get a sense of this when looking at Milwaukee's site where they talk about Standard vs high output batteries. I'd guess the only difference is the cells they use.
With that said, I would be shocked if Bauer required a new charger for the 3ah batteries. Will the tool work? Probably, but it may or may not have the sustained power available to make heavy cuts.
Edit: Check this out