It's been chewed over here before. My guess is that the city didn't want to spend the money needed to buy more r/w or move things into the Cowells Beach parking lot, which would have allowed the rail line to be farther off to the side or more into the middle - both of which would allow bike crossings to be at a better angle.

The final version of the Healdsburg roundabout looks pretty good, really. And even if SMART becomes, some day, something resembling real transit, they won't run through Healdsburg often enough (and NWP is unlikely to have long enough freight trains, even if they someday get back to Willits) to tie up traffic for a long time.