Why does the planting window put my companion crop next to the main crop instead of on it?

Because the window’s Crop Map tab looks for free beds, so it steers the companion away from the main crop. Place companions from the Crop Map instead: it takes one drag, and the main crop stays exactly where it is.

On the Crop Map, click Assign Planting, choose Interplanted in Filter, then drag the companion onto the main crop’s bed. Every bed accepts it, even a full one. The steps are in Place interplanted plantings on the Crop Map.