Are IR phototransistors always dark, are IR LEDs always clear?
The dark part of the IR phototransistor is often called daylight filter.  It's there to make the IR phototransistor less sensitive to visible light.  (Be aware that the sunlight has got plenty of IR too.)

I have looked up two phototransistors: both are made by the same manufacturer, both have the same mechanical package, both have peak sensitivity in the 900nm to 940nm region.  One has got clear lens, the other one has got a daylight filter.  Let's compare them.  Notice that the dark one is less sensitive in the visible light region.



(datasheet)



(datasheet)