I am trying to dig through this myself, but I do not quite understand this. It might be related to the Low-Level Notebook Structure described also a bit in the tutorial Representing Textual Forms by Boxes. If you look with CMD+SHIFT+E on those structures you can see things like InterpretationBox and TemplateBox.

ColorData["Rainbow"]

InterpretationBox makes a formatting structure whose interpretation is not based on its appearance. For example, lets compute these:

Plot[Sin[x] Cos[5 x], {x, 0, 15/4}, PlotTheme -> "Minimal", Filling -> 0]
Integrate[Sin[x] Cos[5 x], {x, 0, 15/4}]

and now pack them as

Now the last output is interpreted as the expression in its second argument:

I doubt this is really helpful. I also would be curious about user-built case for such structures.

Anyone from Wolfram that could give me some insight? Surely there must be a function under the hood that can accomplish this...

@Leonid Shifrin @Vitaliy Kaurov @Jon McLoone @Michael Trott ?

I didn't know about CMD+SHIFT+E. Very interesting structure indeed... I'll investigate a bit more, thanks a lot!