Glass, clay, and most metals (aluminum, copper, brass, steel) and woods (hard woodpipe bowls, corn cob pipes) work fine for pipe bowls and downstems. For pipe bodies I try to avoid metal; it conducts heat far too effectively and can cause you to burn your hands.
For actual pipe bodies that won't contact flame, acrylic or other plastics are acceptable; the real reason people don't use them is because they have a tendency to absorb the tars and oils from the smoke and therefore are really really hard to clean. If they are heated up they have a tendency to first soften and then outgas all sorts of nasty shit.
Smoking out of aluminum cans is bad because they are coated with a fine film of plastic to prevent food spoilage/reactions from the acid in food with aluminum. In addition there are dyes and paints on the outside that shouldn't be burned.
The correlation between aluminum in the brain and Alzheimers is just that, a correlation. It doesn't mean that exposure to aluminum will cause Alzheimers, or indeed even increase your risk thereof. Moreover, aluminum and aluminum oxide are not volatile or adsorbed by the human body under most conditions. I would be more concerned with the usage of alum in pickling and deodorants before I worried about smoking out of an aluminum pipe.
Reasonable homemade pieces can be made as long as you avoid exposing smoke to things that will adsorb it, like plastic, and keeping heat away from any plastics or sealants you do use.