Mine's bolted through both layers without any spacer. I have the Kuryakyn one, not the Honda one.
What I did to protect the helmets inside: Get the felt pad circles with adhesive backing (for attaching to the bottom of table legs to protect the floor) and stick those suckers to the bolt head/trunk liner:

The Kury rack came with dome-headed allen key bolts instead of a hex bolt:

It's been mounted for about a year now with no leak problems, but I used clear silicone sealant when I fastened everything.