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Isn’t the “no flag” boat just an urban legend? Never seen one of them Shortest distance on San Saep canal boat is a single digit fare, but I don’t remember if 8B or 9B. Also you forgot to mention the San Saep tourist boat which goes from Khao San Road straight to Pratunam with stops at Golden Mount, Bobae Market and MBK. Boats are big, slow and safe but infrequent and incredibly expensive – 200B day pass, no other option.
I remembered seeing the no flag boat before in the very early morning. Maybe you can try your luck again next time