I think he left out the brass standoffs and just left the area behind the screw holes empty, with brass standoffs in the places that could be lined up. There'd be no possible way to secure the motherboard without at least one brass standoff in place. And unless there were at least 3, the motherboard would mount at an odd angle to the back panel, and possibly be cracked by the force of the screws and mounting devices on it.
Anyway, the nylon standoffs (spacers is not the right term for them) are included because there are times that they're good to use. Sometimes it's hard to get a screw into place, and easier to just put a nylon standoff in place, especially in corners where there's little force being applied by installing or removing things (a nylon standoff can't prevent flexing when you PULL something from the board). It's also common to lose the brass standoffs or run out when working on cases that didn't come with any so you have to use your own stockpile. Some motherboards may also just have more holes than you have brass standoffs. I've also ended up using a nylon standoff in one case where I broke a brass one off right at the level of the panel, no way to grip it to get it out easily.
In general, brass standoffs and screws are the best thing to use. The nylon isn't intended specifically to prevent grounding or anything; nylon is just cheap and effective and metal standoffs would be harder to use due to the "flex clip" part that goes through the board.
Ah, seeing your reply. I assumed you'd used many different cases. Most cases have a board panel that requires using standoffs to raise the motherboard to be level with the I/O panel. Some cases, especially cheaper ones, have a standoff built into the motherboard tray that replaces the need for a standoff. Nylon standoffs are included so that if you have a board that uses holes in different places than those standoffs, you can use the nylon ones.