Well that's the point of a trade study: look at the cost/benefit of different gasses. Obviously one of the costs would be the increased engineering um...pressure put on the capsule design.
Your gut feeling is probably right, though, at least for this length of trip. The increased cost of a different tube gas probably won't outweigh the benefits of arriving 5-10 minutes earlier.
Now if there were a cross-continent Hyperloop system, then for segments of the trip it might be much better to have a different gas. But again, it might simply be better to invest in better vacuum pumps for certain legs of the journey to get lower drags and higher speeds.
The only ones I see that are significantly higher than nitrogen/oxygen are methane, hydrogen, and helium.
Helium is mondo-expensive. It's not cheap even in welding-tank quantities, much less in the amounts you'd need here.
Hydrogen is flammable and/or explosive (depending on mixture) and is a huge pain in the butt to keep confined (so is helium).
Methane is cheap (but not as cheap as air :-)), and we have lots of experience with keeping it confined in big pipes. However, it's also flammable or explosive.
Using anything but air is going to require some sort of complicated replenishment/purging system and an air lock at both ends, whereas air leaks just require pumping it out again.
Your gut feeling is probably right, though, at least for this length of trip. The increased cost of a different tube gas probably won't outweigh the benefits of arriving 5-10 minutes earlier.
Now if there were a cross-continent Hyperloop system, then for segments of the trip it might be much better to have a different gas. But again, it might simply be better to invest in better vacuum pumps for certain legs of the journey to get lower drags and higher speeds.