The 2n3904 will do nothing except keep the RCD-24 from working.
Back to basics: According to
this data sheet:
if the led driver is to be pwm'ed directly using pin 3, then the pwm pulse train frequency should be 200Hz or less. The PWM produced by the Arduino library is ~500Hz (too high), so you could directly drive pin 3 if you write your own bit-bang code to generate a pwm signal out of the Digispark at about 100Hz.
Alternatively, use the analog input to the led driver and the existing PWM function in the Arduino library, but put a low-pass filter between the Digispark pwm output, and the led-driver's analog input pin 2.