The first line states that the initial data copy will _only_ copy filtered / relevant data.
While warning, but also elsewhere in the documentation it is stated that initial table _does not_ respect any publish limitations.
Hence the conflict.
"publish" is a setting, it is completely orthogonal to the ability to specify a "where" clause.
A where clause is always applied, both for the transfer of the ledger table data and the transfer of journal event data. The publish setting can only ever apply to the transfer of journal event data by its very nature.
