I attempted to set the option compact in the DT::datatable that is rendered in a flexdashboard. It does not result in a compact layout like the example in the documentation. I have a github repo with instructions to quickly recreate it using included scripts. You can see the dashboard here.
documentation example of a compact datatable here
Data
#dm_table <- datatable(dm_2013_df)
dm_table <- datatable(dm_2013_df, options = list(hover=TRUE, compact=TRUE))
dm_table