One behavior of Table To Table—Conversion toolbox | ArcGIS Desktop, Copy Rows—Data Management toolbox | ArcGIS Desktop, and most other tools that are designed for tables and table views, they ignore/exclude/drop the geometry column when run against a feature class or feature layer. I find the behavior quite intuitive and handy since it creates an easy way of dumping all of the attribute information from a feature class into a non-spatial data format.
Unfortunately, TableToNumPyArray—Data Access module | ArcGIS Desktop treats a feature class the exact same way FeatureClassToNumPyArray—Data Access module | ArcGIS Desktop treats a feature class when passing the all-fields wildcard, "*", which is it exports an (X,Y) tuple of the geometry column. Not only is this behavior inconsistent with most other tools that operate on tables, it is inconsistent with the documentation of the tool:
Geometry, raster, and BLOB fields are not supported.