I have only one villager currently set to prefer Farming, but it seems that the two others who rank as Master Farmers come help him out more often than those who don't have as much skill. This is more evident in the harvesting periods than in the watering times. Is this a quirk or a design feature? I don't think I'm merely imagining this.

You didn't imagine it!
And it's the same with the other skills. The Masters often work by themselves on their "favorite" job!!

On a tangent:

After multiple failed attempts at my prompting, a couple went indoors entirely on their own--and immediately produced a child.

While this is not a realistic simulation, occasionally some aspects . . .

Yes that what happens after they got some improvement in parenting

Or if you choose them to be parents as their major activity.

with my villagers if they were a master at farming and trainee at buliding they would always want to farm

Yes, that's true. Even if you try to change their interest (like make a master farmer build stuff), the master always end up doing some of their favourite task (the one they've mastered).