I have noticed in ArcGIS Pro 3.5.7, you can add fields and use tools that add fields when interacting with feature classes in a geopackage in the Catalog Pane or Catalog View. Interacting with a feature class in a geopackage through a Map treats the feature class as read-only (a warning is visible when trying to add a field through the Contents Pane).
Currently, file geodatabases support things like datasets, attribute rules, topology, utility networks, parcel fabrics, domains, and other Esri specific functionality. I think the another difference is file geodatabases are able to compress the geometries stored and geopackages cannot.
I am not sure what you mean by "full functionality", but I do not expect geopackages will support any of those Esri capabilities because the purpose of the geopackage format is interoperability between software.
There are also Esri mobile geodatabases which is kind of a hybrid between file geodatabases and geopackages. They do not support everything that a file geodatabase does, but they do support most of Esri's database functionality. Mobile geodatabases are also built on SQLite but use ST_Geometry to store the spatial data.
My recommendation would be to use either file geodatabases or mobile geodatabases and then export to a geopackage when you need to share the data with someone that does not have access to Esri software.
I have to admit that I have never checked out the mobile geodatabases. I need a dataformat that is easy to exchange and still supports the geoprocessing that I am used to in ArcGIS Pro and NULL values. I would like to avoid to switch between formats, because there are often small differences which can lead to unexpected results.
One of the tools that I use very often is extract multi values to points which needs to be able to add new columns to the datalayer, which still does not work on gpkg in 3.7.0. I do not use attribute rules, topology, utility networks, parcel fabrics, domains on a regular basis, for functionality where ESRI has the only built-in solution, gdb might be an option.
GeoPackages also do not support metadata for the datasets inside it. This is my primary reason why I do not use them. I can't document what I have been doing to the data through the metadata editor interface in Arcpro.
That's useful to know, I hope esri include the ability to read/write metadata to a gpkg as that would greatly accelerate my use of them!
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