For what it's worth, the feature was added in 1213 (April 2011) (see
6.0 Dev Notes ), and as stated in the notes, it was supposed to default to checked (i.e. compatibility mode). And it certainly is the case that if you manually remove the setting from your registry configuration (to simulate an older configuration from before that option was added), and then go into the ATE configuration editor, you'll see that it got checked automatically.
However, in testing this now, I see there was a loophole in ATE itself was interpreting the absence of the setting as being equivalent to 0 (not checked), and if you then brought up the configuration dialog from within a connection and saved it, it would then get permanently written to the registry. So I'm guessing that is the sequence of events leading to it being unchecked (or acting like it is).
That will be fixed in 1258.0, which will also include an option in the AG_ATEDISCONNECT command to override it.
Does that cover all the bases?