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It is a good idea to install a magnetic plastic (acrylic) storm window under a skylight. I do this in my own home where I have a large 4 ft. x 4 ft. glass skylight. I use it even though my skylight has thermal pane glass with a low-e coating and argon gas in the gap between the panes of glass.
The clear plastic storm window offers three benefits. First, it creates an extra insulating dead air space. Second , the magnetic seal reduces air leakage through the skylight trim. No matter how well you try to seal a skylight and trim, there still is some air leakage. Third, the clear acrylic plastic filters out nearly all of the sun's ultraviolet fading rays that damage your carpeting and furniture.