You obviously been very fortunate with the the rest of the environments you have worked with, but remember this started as a hobby platform and not necessarily a professional tool. Also, any one can contribute code, libraries etc. to the Arduino eco-system and post it somewhere so the quality. especially in the area of documentation, will inevitably vary.
Most people are happy not to have spend days studying the datasheets of the MCUs populating the Arduino board, where questions such as your watch dog timer problems could be answered. They are happy to find a code example which they can adapt for their requirements. There Google is quite good. But, really, the Arduino layer is a relatively thin layer on top of the MCU, its tool chain with a (optional) boot-loader thrown in, so there is not that much to document.