As far as I know, you only get points for things that are in rooms. Building the Watchtower Blueprint (required by the story) isn't worth any points because it isn't defined as a room. The room points tally does include the points for the blocks that make up the walls and floors as well, and any decorative items that are placed inside those parameters. Windows will count, as they take the place of the wall blocks, and so on.
I got a "Garden" blueprint or room from doing a side quest, but I haven't built it yet. If I recall correctly, it is also walled off. "Bench" is the type of item that determines if a room is a garden. You just have to be careful not to make it too large.
This image may help:
http://m.imgur.com/tq92hvn?r
In my experience, some rooms will not count as the upgraded version until the story requires it, like the ones related to your crafting room.