But ion propulsion's major disadvantage is its small thrust.
It's advantage is that it can maintain that maximum thrust for a very long period, thus enabling the spacecraft to achieve potentially higher velocities than a conventional chemically powered spacecraft.
So I doubt that the 39 day mission is plausible

It can always be piggy-backed on a shuttle or can be launched and assembled in stages. The engine won't be large, the space is needed for human ergonomics.

We're talking about the engine used to provide thrust to a spacecraft traveling to Mars. So we're assuming that the capability of launching the payload from the surface of the Earth has already been realised.
And technically the ISS is already complete. Those new modules and equipments are just to supplement aging equipments and other what nots.

The problem now is that we DO have viable methods of transporting vehicles into space. And now we're not talking about whether interplanetary commute being on the horizon. We're talking about the claim that commuting to Mars is possible within 39 days using ion thrusters.

The world does not revolve around the US.
Although NASA has encountered a lot of problems in recent times, the Europeans launches are getting more and more reliable, with more and more private companies joining in the business. And the only way private companies can complete with national government-backed space bodies is to constantly come up with innovative and reliable methods of launching rockets into space, which solves your problem of first getting the spacecraft into orbit, just in case you forgot what your argument was about.