As far as I'm aware, the basic idea is that the compressor and running gear would all be battery-powered, given that the concept relies on "gliding" through the tube without any contact--ruling out an external power source like a third rail or catenary.

Furthermore, lithium battery fires oxidize themselves--even if the tube were completely devoid of air (which isn't actually the plan anymore), battery fires would still occur.

And finally, the proposed "overhead tube" or underground tube infrastructure makes fire escape much more complicated and difficult. Conceivably, at the very least if you had limited mobility, escaping a sealed steel tube either up or down would pose a significant challenge. Given the nature of historical tunnel fires, even most able-bodied people probably wouldn't stand a chance.

Regarding your edit, yes this is absolutely a fundamental flaw. This is one of the many reasons why from a civil engineering perspective, the Loop/Hyperloop (and similar battery-powered gadget-bahns) are laughably bad ideas.