It might be made to work as you describe. And yes it would pwm the fans. But understand that, if running 64 fans with a max7219 + transistors, the maximum pwm would be 12.5%. Can you try the fans at that level? Would it be enough for whatever mysterious purpose you have in mind?
Alternatively, how about several (6~10) "Adafruit 16-Channel 12-bit PWM/Servo Driver - I2C interface - PCA9685"? You may need transistors for each channel, unless the pc fans are the type with a built-in pwm driver. I think the 4-wire type of fans are like this.