If the value you supply a fan is a relative figure rather than an exact figure this would be the case. From what I understand, when controlling an PWM fan, you supply it with a figure of 0-255 (off to full speed)? If this is the case, then I could send the same value (eg 122) to both the in and out fans of one section (even though they are different fans capable of different top speeds) and this would set them both to 50%?
A PWM signal is a rectangle wave where the percentage of the HIGH value of one cycle is equal to the PWM value. So if you set the value to 127 you should get a PWM signal with 50% duty. The translation of this PWM to actual rotations is done by the fan.
A Mega does sound an attractive option if it will be capable of supplying 25mHz PWM to all my fans from a single device without it struggling, especially if it can also cope with the rest of my requirements!
I don't see any problems here.
Are these easy to work with in terms of programming multiple PWM devices through one of these?
Yes, these chips are quite easy to work with. The problem might be to get one that support 25kHz.