Consider the criteria you would use in evaluating a window. In the case of a transparent window, you would value clarity. You would value being able to see what was on the other side without obstruction. You would almost want the window to be an invisible but protective barrier. In the case of a stained glass window, you would want the color to alter the sun’s light in such a way as to make the room beautiful, colorful, and less bright. You would likely be more interested in atmosphere.
The earliest forms of glass were colored. Colored glass was meant to be looked at. Later, transparent glass came along and transformed glass from something that inspired wonder into something that was extremely useful. Clear glass was meant to be looked through. The scientific enterprise comes in part from the development of transparent glass. Clear windows provide the kind of enlightenment that modernism values. Modernity regards stained glass windows as decorative or ornamental at best and as failed windows at worst because they do not allow you to see the world as it is.
I suggest that these two types of windows represent two different kinds of enlightenment. The transparent window represents scientific enlightenment. Science values clarity, understanding the world as it is, and seeing ourselves as rational minds. The stained glass window represents religious enlightenment. It is interested in beauty, contemplation, and seeing ourselves as souls. Each window is valuable but not for the same reasons.
I do not think the two windows should be in the same room. In other words, I do not think science and religion can be harmonized. In fact, when religious people seek harmonization they operate out of the clear glass paradigm and seek to translate their religious experiences into something that makes sense in the light of day. Fundamentalists and progressives do this, though with very different goals. ZeroTheology attempts to sort out these two different kinds of windows so that we can all occupy houses big enough to have rooms for each.