Point 2 is not intuitive. I went around with Xavier and Blaze a couple of times. It boils down to: choose to be Trained or Confident. There is no cost difference and it does not count against the points or level checks.
Likewise for point 1 we went around a couple of times and the spreadsheet does represent what is intended. Essentially one quater of your modules will be trained, one half confident and one quarter expert.
As a player of RPGs you would expect experts to be a subset of confident but that is not the case. The rule is not “half can be confident or above and of those x can be expert” it is “half can be confident and a further number can be expert”.
It initially seems generous, but it does seem to give well rounded officers who still cannot do everything. There are never enough points. So it must be right 🙂