My preferred option is to put the "chamois" in existing clothes. I use shorts or sweat pants and just sew in the peanut of fleece. Chamois is not my idea of practical on the touring trail. Fleece works well enough, and is easy to wash. Of course if you want to wear cycling specific weird wear, then there is no point in making your own. The advantage to making your own is either to save money, or look, non-idiotic, which is subjective.

Functionally a sewn in pad, without undies means no chaffing from the leg band of undies, or no double elastics at the waist, no double layers except where the fleece is inserted. Much more comfortable for riding. There are reasons why the clothes we normally wear have the form they do, they are clearly not as apt for a situation where you spend most of the day riding.

By the way, there is that ridiculous cotton death fabric thread. Most of the concerns about cotton shirts are a lot less real than similar concerns about cotton undies, if those would otherwise float your boat.