I've had both and much prefer the fiberglass. Fiberglass is more aerodynamic, quieter, easier to paint and to keep clean, generally stronger if you mount a rack or basket on top, warmer in the winter, and almost always better looking. If the choice is between the two units pictured, the fiberglass one gives you more interior volume because of the bumped up roof. I had a earlier Toy and a cab-high shell does not give you much space to move around inside. Those pop-open side windows on the aluminum unit may present some security issues that the sliders on the glass shell don't have. If the glass unit already has a factory carpet headliner in it, that could make the decision a no-brainer if you plan to sleep in it. The headliner eliminates your breath condensation dripping on you while you sleep.
I could stand of top of my ARE. Don't do that with a fiberglass topper!
I have three trucks now with SnugTop fiberglass shells. One has a Yakima rack system that has carried 800 pounds of lumber without failure (the Yakima bars are badly bent, but the shell is fine). Another truck has a shell that will be getting a similar rack system for the same type of use. The third truck has the same Yakima cross bars with a 4.5x5 Con-Ferr basket mounted to it. Mounted to the Con-Ferr are an Ez-Awn Bat Wing on one side and a 16-gallon water tank on the other side, with the basket open for cargo. I have stood on the basket floor for long periods while glassing on hunting trips with no adverse effect on the fiberglass shell. SnugTop and others offer reinforced roofs as an option, but none of my shells have that reinforcement.