sometimes my builder will spontaneously decide not to water the strange dead plants but instead to clear the blockage, which is already done. Is there a second goal there or is she just mental?

The watering of the dead plants is actually a puzzle and will help with a few more puzzles. Your builder will be inclined to water them and they need to to advance in the game. It takes a while though so be patient and let them do what they know they have to do.

yep, I actually have gotten past that. What I'm surprised about is the "clearing blockage" after it's cleared. It's more likely when I am an impatient old God and air-lift my builders from the dead plants back to the water source because they aren't as fast as I want them to be. But it can also happen spontaneously. I assume that once the blockage is cleared, it's gone, but my builder doesn't seem to think so.

You needs to go into details and check the box next to the tech that you want to be the main responsibility of the villager.

I've had that same thing happen - the builder continuing to move rocks from the lagoon after it was cleared. Once the field had been fully watered however, he stopped.