Although you refer to “stained glass window” and “glass window” in your question, I believe that the proper terms are “stained glass ceiling” and “glass ceiling.” We speak about “ceilings” rather than “windows” to indicate that the people below the ceiling are prevented from rising to a higher level. If we speak of people on different sides of a window, we would be implying that they are on the same level and are therefore equal. This is not the case.
The term “stained glass ceiling” is used to refer to the difficulty that women have in rising to high positions in most churches. This term is taken directly from the idea of the “glass ceiling.” The term “glass ceiling” refers to the difficulty that women have in rising to high positions in secular organizations. In the glass ceiling, women can see through the ceiling and know what is above them, but they cannot reach it. The term “stained glass” is simply used because of the fact that so many Christian churches have stained glass windows.
There is really very little difference between these two “ceilings.” The only real difference is that the glass ceiling is a de facto thing—it is not created by the laws of the organizations in which it exists. This is because it is illegal for companies to discriminate against women. In contrast, is sometimes a de jure thing—it is created by the rules of some churches. One example of this is the fact that women cannot be priests in the Roman Catholic Church. There are cases where the stained glass ceiling is de facto and not de jure, but the fact that it can be de jure is the main thing that differentiates it from the glass ceiling.
We can say, then, that both the “stained glass ceiling” and the “glass ceiling” are phenomena that prevent women from rising to higher levels of organizations. There are two differences between the two. First, the stained glass ceiling is found in religious organizations while the glass ceiling is found in secular organizations. Second, the glass ceiling in the US is always de facto while the stained glass ceiling is sometimes de jure.