Katherine,
As long as Business Analyst Desktop is installed and set to block apportionment Business Analyst Pro will use block apportionment.
I do believe it is a logical enhancement to have the ability to set apportionment in Business Analyst Pro especially for the scenario where one does not have Business Analyst Desktop installed but does have the local data installed and using Business Analyst Pro. I will go ahead and log one on the Esri Support side.
I did go through another round of testing focusing on running Community Profiles but this time not using local data. Also tested uploading a shapefile to BAO (Fairfax County) as well as a web map version and these reports all match each other (though 2019 population was 4 people difference compared to locally run Community Profile which is an acceptable difference) as well as testing online reports on the ArcGIS Pro side both feature class and web map layer.
Infographics on the ArcGIS Pro side with 2019 population also lines up with numbers in the above paragraph.
In your original post what was the source for the Fairfax County polygoon you were using?
Regards,
Jason R.