Well, once the thing was built you'd expect that particular task to be quite easy. An airtight tunnel surrounded by kilometres of rock - not much air down there in the first place, and you'd just need some effective airlocks on the ends.
Not to downplay the size of the task, of course; it would be an astonishing feat of engineering and probably quite out of our reach for the foreseeable future, at any kind of reasonable cost anyway. The tectonic boundaries, as you say, would present a particularly challenging aspect of the project. However, theoretically it's probably the most efficient way from A to B on our little blue marble and so no doubt it'll be done eventually.
Not to downplay the size of the task, of course; it would be an astonishing feat of engineering and probably quite out of our reach for the foreseeable future, at any kind of reasonable cost anyway. The tectonic boundaries, as you say, would present a particularly challenging aspect of the project. However, theoretically it's probably the most efficient way from A to B on our little blue marble and so no doubt it'll be done eventually.