I think it would be a pain in the butt to make dropout alignment tools when a set only cost $80.
Here's a link to photos though.
http://www.parktool.com/repair/readhowto.asp?id=40
Answer to 2nd question is no. It is an result of the machine that cuts the threads into cast or forged parts not being perfectly parallel to the axis. Not a problem as they allow a certain mfg tolerance for this.