My best guess: In case there is only one title in the playlist you do not want it to loop forever, your brain needs a break sometimes. Also, I thought that this was something from the script-coded music system (there is one, too, iirc), so I was surprised that this comes from the engine.

The ambient music system was devised in a long and complicated process between Sven2 and ala.

Like Clonkonaut stated, it was the result of the ambient sounds and music conception, and was done intentional.

I definitely agree, that the breaks are annoying and don't work out like we have planned. That is probably true for the whole ambient system.  I guess it was supposed to be the first version, but never developed much further, I also didn't leave much feedback afterwards, which maybe would have been important to develop it further.

We envisioned that the music could be enriched by smaller breaks of silence filled with atmospheric sound recordings (like drips of water and cave echoes, animals, wind etc.). Only to be followed by another casual start of the music fading in. Also to not tire out the playlist too fast.

The break currently is pretty long, and feels like a "cut" of the atmosphere. Also we never implemented many sounds for atmosphere after all. We could deactivate it, or try out a small break (10-20 seconds) I guess.

Another problem is the fading and switching of the tracks, isn't too atmospheric either. Especially bad are the alternating cave-sky segments like in Bristle Ridge.
Also if you don't enter the cave for like 30 minutes, but go back in then it still continues a track from the last time you went in, but it is usually so long, that the player doesn't remember the connection. So in that case a new track should start instead.

We can probably improve the system, and make it a lot better.