This might help a bit,
Ken (@sugoi.xv) on Instagram did this mod on his Crosstrek. He said that he drilled the holes on the side and used an led strip inside. To help match the factory taillight, he used a dimming controller to adjust the brightness of the led strips.
I'm not experienced in microcontrollers or arduino, but you could probably use an Arduino to dim the LED strips by adjusting the PWM. You could probably use two different inputs into the arduino, 1 for the running lights, and another for the brake lights. So that it's a lower duty cycle on the PWM resulting in dimmer LED's to match the running lights, but when you hit the brakes, the PWM could be set higher or to full brightness to match the brake lights.
If you could find or make a thin enough light diffuser, you could diffuse enough to not see the individual led chips. Or go with a set of red COB LED strips.