To finally settle this silly debate (for people who heard that building by alz is better from someone who was told by someone else who was told by someone else who most likely heard it from a lvl100 noob dancing in BI): Here you are. This is your proof that building with points is better for your nation.
The main reason why you all get confused is because you understand "building with points" as it uses your nation score. That is where you've understood it incorrectly.
"Building with points" means using your building points. When you see in TG in your system messages, "xxx points are automatically up", that is referring to your building points. Use building points > Increase nation score. (This is only affected when you actually complete a tower. If you cancel it, no points will be used.
I'm not sure how much more explanation you all need, so I just really pray you'll understand through my guide.
If you can't believe me as a GA, you can believe your eyes when you see my http://imgur.com/a/n9QBW guide :P