Why does the game give you points for stealing the spinach dip and then throwing it in the water? What's the point of that?

Why does SQ4 give points for taking the unstable ordnance from the wrecked tank and then immediately putting it back in (or was that SQXII)?

You can look at these moments as classic Sierra "gotchas". Or you can consider:

1) Sierra wanted to award players for their curiosity, for carefully scrutinizing everything and taking everything not nailed down. So point awarded.
2) Sierra wanted to test players' abilities to recognize when their actions put them in danger, and award points for taking corrective actions to rectify said danger. So another point awarded.