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I am replacing the whole unit that the fuel pump is attached to. On the old one, there is a box in the middle of the wires coming from the top of the gas tank and connecting to the fuel pump. On the new one, this box does not exist.

In the image, this box is circled in red. The fuel pump itself is removed.

Is this an important piece? Does it have something to do with the supercharger on my 98 SSEi? Should I even worry about it?

Well I've since put everything in the tank and installed the tank back in the car. Some of the quick connects on the fuel lines were totally destroyed because the lines rusted up inside them, so that was a hassle but... It's finished!

And as far as I can tell, there is no downside to not having that little box in there. The car is running better than ever! My fuel gauge even works, which is very exciting. Yay!