The courtyard and the silkscreen are different things.
The silkscreen is visible on the board, the courtyard is a design concept and visible only in the PCB Design Application.
Generally the silkscreen outline is slightly smaller than the courtyard outline. Courtyards can touch each other, so if the silk outline would be the same, two resistors would have a shared silk line if their courtyards touch. So the silk line must be a bit on the inside of the courtyard to make sure that there is some space between the silk lines of two different components as you see on boards.
The silk outlines and courtyards are suggested by the IPC-7351C document. In IPC-7351B the courtyards were rectangular, they can now be "arbitrary" and more closely follow the component's outline. The silk outline for resistors, diodes and capacitors are not rectangular either.
Below you can see a detail of one of my boards. I haven't updated the outlines of all my components yet - the lines in blue are the silkscreen lines, the lines in grey are the courtyards. You can confirm that this is inline with my explications above.
Ben Voigt's remark caused me to look in more detail. The picture has some cases where the shared lines are larger (around the crystal) and other cases where the lines are smaller (between the columns on the far right).
So it seems that the designer may have done one or more of the following:
- Not use courtyards and only had silk lines, using them as some kind of courtyard;
- Not respect design rules if he did have actual courtyards.
- Had overlapping "courtyards" (for the cases where the silk line are smaller) - and this resulted in the production files being automatically adjusted to avoid having silk on the pads (these adjustments may be made by the PCB design tool, and are in my experience also applied by the manufacturer).