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I'm not familiar with this device, but it is possible that different variants were made or were possible with the same PCB.  Consider the documentation you have as general guidance, not necessarily exact.  I've seen this a lot with old devices like that.  (New devices solve this problem by not providing any documentation.  Much better!)

The diagram does show the analog and digital grounds tied together, but it also shows the 5 V digital supply coming from a separate secondary, not just another tap from a single secondary.  It looks like maybe the 5 V supply was originally intended to be isolated, but that in later units they decided to use a single common ground.

Go with what you've got.  I'd try to power an add-on device externally anyway.  In other words, don't use any of the supplies from this device.  Use your own.  I imagine you want to interface this device to a computer, so having your interface circuit get powered from the computer's USB seems like the obvious thing to do anyway.