Have right-mouse-button-pickup-color also pickup transparency

That might be a good idea if done right, although there are some issues.

Drawing with transparency could either set the transparency of the drawn pixels absolutely, or it could blend with the color in the layer. I think the second behavior is the most useful one, but that means drawing with a fully transparent brush would have no effect.

Also, it simplifies things to only pick opaque colors. At the moment the picked color is the visible "flattened" color of the clicked pixel, not the actual color of the pixel in the current layer. I think this is more intuitive, and it might be frustrating having to change layer to pick another color.

One solution would be to switch to the eraser tool when you pick a fully transparent pixel, but that seems a bit weird.

Yeah, I suspected as much. It would be a 'useful hack' for drawing sprites on transparent backgrounds, but not more than that and not worth all that complexity (feel free to close/remove this topic).

I might make this an option though. For example holding Shift could pick the absolute color in the current layer, and the pen could have an option to disable blending. It might actually be very useful in some situations when you want to have precise pixel alpha values.