How do they deal with thermal expansion on traditional railways? Same problem no? The track needs to expand, they spread across miles and miles and I never saw a damper area (except that the tracks are disjointed by a quarter to half an inch each, which would be the same with a tube in a tube configuration)...
Most modern railroad use continuous welded rail, so there are no joints like what you're talking about. This is both stronger and quieter, but it can lead to problems when the temperature is too high or too load, because of thermal expansion.
"There are a number of ways to increase the resistance of rail to buckling. The first and most common is the use of rail anchors to limit the longitudinal expansion of the rail. Anchors come in a variety of designs, but they all apply several thousand pounds of clamping force on the base of the rail. When applied properly against each side of the crossties, the anchors prevent expansion of the rail in the longitudinal direction." - http://www.interfacejournal.com/features/03-05/track_bucklin...
The choice of Rail Neutral Temperature depends on the region. In the US Midwest and plains it's typically around 95 to 100 degrees. In the UK it's stressed to 27°C (81°F), which is the mean summer rail temperature. In neither case is it the maximum possible temperature.
You don't want it to be the maximum possible temperature for the area, because a well-laid track can be in temperatures 40 to 50 degrees above the RNT before it starts to buckle, and a higher RNT is harder to achieve.
Nor do they lay the track or heat it at the hottest possible temperature. They achieve the RNT by stressing the rail. The RNT can also change over time, for example, if winter causes a curved track to become a bit more shallow.
I agree with you and with the linked-to author: I don't see how the proposed hyperloop system can ever economically handle temperature expansion, and the lack of a good explanation or discussion makes it easy to dismiss the seriousness of the proposal.