A very valid and appropriate talking point here. I haven't been pleased with the total accuracy of JobScan either. However, I believe it can serve as a basic litmus test for a document compared to a job posting at face value. I prefer practicing with phony applications for job postings. I'll test resumes with text boxes and shapes (items deemed decorative by most ATS) by "applying" for a job through Workday, Taleo, etc. and see what populates in the field requirements and what doesn't. This is a good indicator of what is and isn't being read.
Context is also key. Obviously, if I'm emailing my documents directly to a manager for their review, I know that I won't be playing with ATS. That's when I am more generous with visuals like text boxes. The more technically savvy will screenshot images and lay them over text (hiding the text which will be read by ATS) for the visual impact without losing ATS readability.
The most important thing is to stay connected with others and talk about what they are/aren't seeing in best practices. I hope this was helpful. :)