Technically there are two kinds of system generated indexes: the ones that are created with a name in the catalog (it's a generated name, easy to identify as such) and the ones that are only created in the column store table data structure but not in the catalog.
Examples for the later would be concat attributes, inverted indexes and extended primary keys (more than one column in a primary key).
These can be found by explicitly checking for them in M_CS_ALL_COLUMNS.
For the row store, system generated indexes can be created. Again, the name of these indexes makes them clearly identifiable.