their method allows for pwm, they may have chosen not to enable it in software.
since this is a matrix, not a huge gob of discrete leds, there is no way to pwm a single led. you have to pwm one column at a time, and then single out a discrete pixel by strobing the row drivers. this is a software problem, not a hardware problem.
I have a pdf at home that I will post for you later, it details using time domain division to achieve variable brightness in led array pixels... I think they only talk about monochrome displays, but the same principals could be applied to a rgb display.
EDIT:
I've attached the pdf I wrote about earlier, it's by HP (Agilent), and covers a great deal about RGB matrices and even talks about some intelligent driver chips for them.