I used hard maple blocks to provide reinforcement and to align the saddles on the roof rack bar.  The blocks extend down to about 1/4" from the bottom surface of the bar.  I made the channel about 1/8" wider than the bar for a bit of side-to-side play.

The alignment on the bar was one of the things that I wanted to do better than the Thule saddles.  They were always slipping around on the bar.   These saddles should stay put.