Are all the processing steps of tofu harmless?
Making tofu for mass production and consumption and making tofu at home generally follow the same procedures.  Soybeans are soaked, ground, and cooked.  The resulting "milk" is separated from the soilds. Then a coagulant is added (either salts, acids, or enzymes depending on producer and type of tofu). Finally, the tofu is pressed.  The one difference between tofu you purchase in a package and tofu made at home is that the mass-produced variety likely goes through a pasteurization step.  In general, this is a process that has been used for centuries (other than the pasteurization, of course, which is more recent technology). Given the history of tofu production, and the number of people who consume it, any health concerns would have been identified by now.