Yes, I did install longer bolts – 6 inches. I had to deepen the bunks with strips of oak board in order to clear the trailer’s fenders. Others have used hockey pucks. My method has served me well.
I installed them as the manual directed and bolted underneath the trailer. Your installation will be much stronger if you drill completely thru the trailer rail.
I bought my ss carriage bolts from amazon.com: https://www.amazon.com/gp/product/B01M2TWNVR/ref=oh_aui_detailpage_o04_s00?ie=UTF8&psc=1