Axial compressors aren't the only compressor design. Rotary vane compressors have no problem with those pressures.

The internal pressure was chosen explicitly because it was easy to maintain with simple, single stage mechanical vacuum pumps (see Figure 13 on page 22). Heck, the first result on Amazon for "vacuum pump" goes down to 5 Pa. https://www.amazon.com/dp/B012CFTYX4/

Compare the Hyperloop to true "vacuum train" designs, which need to run at 1/1,000,000th of an atmosphere to mitigate sonic booms (an alternate way to get around the Kantrowitz limit). This requires multi-stage pumping with mechanical roughing, followed by turbomolecular pumps and cryopumping. That 1000x harder vacuum takes 1000x as much pumping power (not because the differential pressure is meaningfully different, but because you expel 1000x less air per stroke).