Ian,
For the definition query, if the layers are in the basemap, they will not be honored and you will see everything. Definition queries do work for operational layers (layers that are not in the basemap).
This blog post goes over the basics of using Pro to create a map https://community.esri.com/community/gis/applications/arcgis-pro/blog/2018/01/20/use-arcgis-pro-21-to-make-an-offline-map
Just for context in reference to basemap.
In regards to zoom scale, should be free to zoom, I am not sure what would cause it to be limited. If you can share you map with me, I would be happy to take a look and figure it out.
Are you using a basemap in your map?
What coordinate system are you using?
Mark
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