The points you noticed confused me as well. My (very strong) gut reaction was that obviously Dumbledore is behind it all - he is the one with most control about the wards, and he is the one who gives both the readers and the participants of the meeting the information tha the wards point to the Defense professor as culprit. Also, the line about the heir triggered a mental alarm.

As I said, this was a gut reaction, and it has been quite some time since I read the rest of the story - this is just based on chapters 90 to 94, and the general impression I got from the story so far that this Dumbledore is definitely very different from canon Dumbledore.