The Atheros EEPROM Tool produces two kind of dumps: the first one is the dump you can make, starting the tool in GUI mode (which is full EEPROM dump), the second one is the 512b dump, taken from the command line. I've compared them both and it seems they are different, the data from the 512b dump can't be found anywhere inside the big dump. My presumption is that both are taken from different areas on the chip.
You know, I was able to make the Atheros EEPROM Tool to ignore the Vendor code by some changes in its source code (included in the archive), but that wasn't enough. It seems there are additional checks in the driver that's being used by the tool. Its source code is included too, but it's totally unfamiliar to me.
You said that your card works in Linux. How exactly did you do that? AFAIK, you should add the new IDs in the ath9k source code and then blacklist the kernel module that would be loaded with these IDs (in this case maybe ath10k).
May I ask you about the changes you've made in that code (the tool code and maybe the ath9k code)?