Jeff,
As you experienced, ArcGIS Pro by default saves with relative paths.
However, this can only be done for those datasources that reside on the same drive as the *.aprx document. All other datasources will be saved with absolute paths.
E.g. take a look at these three situations:
- If the aprx resides on W:\, and the datasources (e.g. file geodatabases/shapefiles) as well, all the paths in the aprx will be relative.
- If the aprx resides on W:\, and some datasources reside on W😕 as well, but other datasources of the same project on e.g. D:\, then the datasources to W😕 will be relative, but the datasources pointing to D😕 will be absolute.
- If the aprx resides on D😕 but all datasources on W:\, all paths will be absolute.
I think your current confusion arises because you have a mixture of the above situations, with some ArcGIS Pro project documents having mixtures of relative and absolute paths, others only relative paths, and others only absolute paths.