Also let me add, this would be placed under skylights inside to create an insulated cover to the "skylight" well in the ceiling.

I don't think that you will get much light through the phosphor coating in the tubes. The phosphor isn't made to allow light to pass through, it's made to emit visible light when struck by the ultraviolet light generated when an electric current passes through the mercury vapor. So, even if there were only a couple of layers of tubes, it wouldn't allow much light to pass.

As far as the insulation value of your proposed arrangement is concerned, it would probably be worse than just an air gap. Glass is an very good conductor of heat. Thermal pane windows work because the two sheets of glass are separated by air or argon. The panes don't even touch at the edges. They would have to be very thick panes of glass to contain a vacuum. Argon gas is less conductive than air but equalizes the pressure. So, it's more energy efficient.

I have heard of people using layers of clear bubble wrap as an insulator in between two window panes. The larger bubbles are better. It may not be as superefficient as aerogel. But, it's cheap. It doesn't hurt to add an E film to the outside pane also to reflect heat out in the Summer and back in the winter.

(By the way, the phosphor is also poisonous if you break a fluorescent tube. There is just a tiny drop of mercury in the tube.)