The alternator is absolutely on the battery circuit with the Diode Bridge separating the battery circuit from a ground through the windings. Not just a crack pot Theory but real trouble shooting. My 1200S had this same problem last year.
??? Re-posting the wiring diag here, with Alternator identified. Note the 40A fuse feeding the Alt right next to the 30A fuse I indicated as the offending circuit....if I pull the 40A fuse to the alternator, the .29A current drain still exists. I cannot see how the Alt in this case is still a likely suspect, although I WOULD like to know more about your similar problem and how you solved it:
