Call me crazy if you'd like but when I reroofed my house, I decided that roof glazing was a terrible idea. In the summer you get too much light and way too much heat. My bathroom figuratively felt like an oven in the house. In the winter, the bathroom became the coldest room in the house. I realized this thing is hurting my energy usage and comfort in a significant way.
I had the skylight in my bathroom removed when I reroofed my house. Initially with the reroof I shoved a chunk of R10 XPS in the gap and used temp caulking around the foam to create an air seal. That winter I was comfortable in the bathroom and whenever I took a shower in the winter, I wasn't getting water condensation dripping down the floor. Fun thing I found is that the drywall shaft around the skylight had a product called Thinsheath or some similar name to that, stamped with R6 on it. It it isn't obvious, this big shaft facing the highest point of the house, including the attic was not helpful in the extreme heat or extreme winter. Heat exchange was high and I'm glad I got rid of the skylight. With an 8 watt LED in the bathroom providing plenty of light, I can't see the advantages of using a skylight, even the 'light tube' types, especially since they are rarely installed with insulation.
I guess in the end, if you have one, you are stuck with it until you reroof if you don't have spare shingles that are available or if you don't know how to do the work properly. I prefer to produce my own light with efficient means because daylighting has a high cost of heat when you don't want it and when you want warmth you are exchanging the indoor heat with the outside through the glass. Skylights are even worse because they face the sun in the summer and boil you out. In the winter they are covered in snow and useless a majority of the time. I don't miss mine, I now have a comfortable bathroom.
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