Average reference lines work by averaging the values of the marks on your view - if your bar chart has a 10 bars, it is the simple average of those 10 values; if the bar chart has 1 bar, it is the simple average of that 1 value (which tends to be the same value). The idea is that these reference lines are responsive to the view, but they do depend highly on the level of detail/granularity used in the view.
It looks like #2 is a average checklist % of responses, whereas #1 is a total % of responses. The difference might suggest the difference between the overall response rate vs how well the user completed each question with the the survey.
Thank you so much, Wilson. Is there any calculation that I can use to reflect the average as one value (the average of all the 10 values)?