That calculator was likely written to model systems that were well below choked (sonic) flow velocity. Since it does not take into account those limitations, the results fall apart at anything close to what we see in an airgun. That calculator is probably only taking friction losses into account. By entering very large pipe diameters, with a very short length, I was able to get that calculator to display air flow velocities that exceeded the speed of light. Most of us would agree that is not possible.
Mass flow rate becomes choked at the speed of sound. Though peak velocity can be higher than that since the air can also be expanding as it is flowing. The maximum velocity front ends up being about 2x the speed of sound of the propelling air.
Mach velocity in helium is much higher than air, so it would have a higher velocity limit. But it’s main advantage in an airgun is it’s much lower mass. In higher power airguns, the mass of the propelling air can exceed that of the projectile, even at speeds as low as 950fps.