Probably the best way to learn about these types of things is to visit a flute workshop and actually see some of the work being done. I'm not Micron or Joe, but I think I can still answer your questions for you.
1: In the past, flutes were made with a seamed tube. This is where a flat piece of metal is rolled into a tube, and soldered. Today, most flutes are not made with seamed tube (Altus, as well as some smaller makers do still offer seamed tubing as an option), but rather start with tube that has been drawn from a flat disk of metal, which means that no seams should be visible. For drawn toneholes, a small hole is made in the tube where the tonehole will be, and a small ball is placed below it. This ball is then pulled out, creating a tonehole, and the top of the tone hole is rolled over to create a smooth surface for the pad to seal on. Soldered toneholes are made independently from the flute, soldered on where the maker wants a tonehole, and then a hole is drilled through the tube in the center of the tonehole. One website that you might find interesting is
http://www.yamaha.co.jp/edu/english/factory/fl/fl_001.html It describes and illustrates some of the steps involved in building a flute, and includes some photos.
2. There are varying levels of handmade-ness, and no definitive amount of the flute must be handcrafted for the maker to call it handmade. In the very best flutes, all the parts are made specifically for one instrument, by hand, but some instruments are also called handmade that have only part of the flute actually made by hand.
Hope that's helpful!