Yes, those 9 raised notches take the place of stand-offs.
The manual says not to use extra stand-offs if you were to be using a ATX form factor because of very logical reasons.
The extra space that will be between the Backside of the Mobo and the backplate will/may cause you to nick the edge of the ATX with the PSU or ODD it may also interfere with the socket spacing/placement for the ODD for power and SATA connectors.
Yes, that case does not require you to use standoffs for an ATX form factor board.
The raised notches coincide with the holes for mounting an ATX Board.
Where as the stand offs will be required to be put into other holes to get the placing of other than ATX form factor boards into that case.
Check PIC 4-1 of the user manual.