Hi Gil,
Your post reminded me of this function - one I had never used. Adding bridges to my channel map took bloody ages, so I wish I had found this earlier. Anyway, I just tested it on my Kharkov map and it populated nearly all the right bridges, except a few. I did a little investigating and I've worked out that the engine is looking at map_t, and wherever a road, rail or highway pixel lies over a RGB 31 pixel (i.e. CoastRiver) it will place a bridge. So, bridges don't work automatically in cities because they don't have CoastRiver tiles.
So, to do this, make a copy of your map_t. Load the map and wherever you have rivers in cities or woods etc line the banks with CoastRiver. Save and exit, transfer the new map_t, reload the map and then use the Create Bridges function. Then, once bridges are in place get your original map_t back and you'll have bridges everywhere, including in cities.
You know I'm so glad you posted this, because I wasn't aware of this tool (in fact I bet most map makers aren't) and I really wasn't looking forward to manually adding bridges to my Kharkov map.
Joe