Completly, agree - there's a real lack of clarity when it comes to documentation of some tools and options. And it's only trolling through dozens of forum posts on any number of issues that you can begin to troubleshoot common issues. Example workflows won't resolve those headaches but the following resources may help you get started.
If you're looking for a streamlined yet comprehensive explanation of GATK4 and the main Best Practices workflows, you may be interested in the O'Reilly book I co-authored called Genomics in the Cloud. (The cloud part is secondary, all the GATK-focused explanations are applicable pretty much regardless of where you will run the workflows).