Does the "Executing Jobs per user" governing setting also apply to Datasets within Documents/Dashboards?
Yes, Datasets are subject to the the "Executing Jobs per user" governing setting. This is by design, as datasets are separate reports that feed into a larger document/dashboard's analysis.
This setting can be found in Project Configuration -> Governing Rules-> Default -> Jobs -> "Executing Jobs per user"

To test this behavior:
Note: If the datasets are sourced from Intelligent Cubes, this governing setting does not apply to those specific datasets. Since the job directly executes against a cube, it does not create a query job.