It's because of IMAX
SlashFilm reports on an exclusive interview with Tron: Legacy director Joseph Kosinski, where he revealed that certain scenes in the film were re-sized for IMAX screens; the intent was to show these scenes only in IMAX theatres, but evidently they made it onto the home media release as well1:
Kosinski revealed to me that five action sequences from Tron Legacy will be shown in 1.7:1 aspect ratio, exclusively in IMAX Theatres.
If you've ever seen a theatrical 3D film on the IMAX screen, then you know that the movie doesn't fill the whole screen, leaving huge bars to the top and bottom. With The Dark Knight, Christopher Nolan shot a few sequences and establishing shots with IMAX cameras, allowing the screen image to switch aspect ratios and fill the entire huge IMAX screen. If you pay to see Tron Legacy in IMAX, you will see something similar.
Most of the film will be presented in widescreen, 2.35:1 aspect ratio, like it will be in your normal multiplex screen. But in the IMAX presentation, five special action sequences are being rendered at 1.7:1, which means that you will see a lot more on the top and the bottom.
As that last paragraph hints, IMAX is shot in a different aspect ratio, which is what causes the "black bars" to appear and disappear; your screen is configured for one aspect ratio, so it has to compensate when the ratio changes.
There appears to be no narrative reason for why those particular scenes were chosen, which rather puts paid to your theory; rather, they seem to have just chosen the five most high-octane action sequences.
1 I don't know what format you're watching this in, and I don't have the DVD myself, but there have been complaints about this effect in the iTunes version, and reports about it on the Blu-Ray