Audio Tracks With Partial Clips

The current project I am doing runs 104 minutes, with one standard audio track (A1). The first and last 20 minutes need an audio commentary, and the last 10 minutes need a third audio track (it's an alternate mix, basically).
Rather than creating three separate timelines (obviously, for space reasons -- not to mention efficiency), I have the main audio program on A1, as well as partial clips in A2 (commentary) and A3 (additional audio). However, since A2 and A3 only apply to part of the program, I am using Chapter Playlists (YAY for these!). As a result, A2 and A3 are audio tracks that have clips in parts, but a whole bunch of blank space in the middle.
I wasn't sure if this would work or not, but it seems to, with one small problem -- I just noticed that when listening to ANY of the audio tracks, when a point in the timeline is reached where one of the other audio tracks hits a clip's in point, the audio skips. It's just one small skip, but it's an annoying little imperfection.
For example, if A3 is blank until its clip begins at 95 minutes in the timeline, and I am listening to A1 (main program), then when I reach the 95 minute mark the audio skips. This also concerns me because it makes me wonder, are there any other problems that may arise when playing this DVD in a variety of players. Does anyone know if I might run into other problems?
I thought that by only putting the audio clip and not filling the rest with silence, I would save space on the disc. (My understanding is that a full audio track - even with silence - would take more space because it's encoded at a constant bitrate).
Am I going about this the wrong way by putting on the partial clips? Or should I just put on full clips that simply have silence in the unused portions -- and more importantly, if I were to do that, would it take up more space?
Thanks!

Did you hear the audio skips on a burned R or RW disc, or just in Encore's preview?
I would expect that "silence" would take up space on the disc. You could test for yourself to see just how much space by creating a test timeline with appropriate silence-d audio tracks, forcing a manual transcode of the audio assets and then taking a peek at the Project and Timeline panels to see how much space they take up.
-Jeff

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