I agree that it should be held in Boston, but before the bid doc came out, I assumed that the Olympic Stadium would be closer to the 70k-80k range. It's seeing the lower capacity that prompted that question. However, I don't agree that T&F is an afterthought in comparison.
I agree on t&f's draw at the Games, and also that opening ceremonies should be at the downtown site.
On stadium sizing, track and field is the huge fly in the Olympics ointment for stadium construction and post-Games re-use and post-Games white elephant avoidance. The track layout is way too wide for football or soccer, so those teams, in any city, don't want any stadium that was built to handle track and field. Oregon university has one stadium for football, another for track and field. Their t&f stadium has about 10K regular seating and can expand to about double that for when they host NCAA championships, which they've done as recently as 2014. That's a college that takes t&f very seriously, but their capacity is way below an Olympics stadium, even when they host NCAAs. And they built something entirely separate (and much bigger) for the football program.
So even a smaller, 60K capacity stadium that is wide enough for t&f is useless to the most likely users post-Games. If you want to implement the partial re-use idea, like has been bandied about for the Revolution, I think you'd want to not just lower the upper reaches, but move one whole side in closer. That's probably a half-demolish and rebuild job, unless it's actually practical to have half a 60K seat stadium be movable. That sounds like a stretch.
The IOC, at least in their official rhetoric, has clued in to this problem, hence their new guidelines for a smaller main stadium, not to mention temporary stadiums or the stadium-reduction concept. It isn't about t&f's relative draw during the Games, it's about the avoidance of white elephants after the Games. the 20K delta is a tiny sliver of the TV audience anyhow.