For an ATX board (The Z87-A is ATX), there should be 9 bumps (or standoffs).
All the screw holes need to line up. Don't worry, they will if you are fitting it in right.
The board is supposed to be grounded against the standoffs (case bumps) and no bits that stick out on the bottom of the board should be able to touch the case.
But to be sure, does the MB fit into the I/O shield perfectly aligned when resting on the bumps, or does it need to be raised further?
Although you can run the board outside the case, there would be more risk than running it properly installed.