When transport once appeared, i tracked it carefully under some magnification (to fit continent to screen), then sent aircraft to exact location (not just to radar range). I managed to ambush it before transport took out (i noticed it previous time, since i waited too long with 2-3 aircrafts constantly in area, as i tracked disappearance location not enough exactly).
As i can see, alien base has just one transport dock. If transport is meaned to be in base during capture, it probably should be recovered as usually done with any land mission.
