Reporting more than one keyboard is required in order to support more than six keys pressed at a time, which is the limit for a single USB keyboard. So no, this would not be possible without work on the USB code. Please understand that what you're asking for is a reduction of functionality (removal of n-key rollover), causing more work for testing, in order to support a system that isn't fully USB-compliant.
My guess is that the cost for this code change is in the 2000-2500 EUR range. If you find enough people who would be willing to chip in some money, we could of course do that. However, if you're paying over 400,- EUR for an FPGA board that has a plain description of "USB supports HIDs", and it turns out later that keyboards with n-key rollover don't work, it feels more like false advertising than the fault of the keyboard. If you provide a USB port, call it "USB Host" and hide the fact that it does not have hub support on page 10 of the manual instead of mentioning it with the online product description, there's something wrong. Many keyboards that support n-key rollover use this trick of pretending to be a USB hub with two keyboards connected.
The good news is that the Nexus A7 100T USB interface is driven by a flash-based microcontroller, so the hardware does support an upgrade path (just like Keyrah V3 does). Granted, implementing hub support (even for just two ports, knowing that there's two identical keyboards connected and no further hub) is more complex than the Boot HID interface protocol only, but it's not prohibitive, as current and not-so-new PC BIOS implementations show.
You are right that "one of the two sides" needs to move. Both involve code changes. My guess is that Digilent has a much higher margin on their boards to cover such code changes. Keyrah V3 is a low-cost product with a lot of functionality, but low margins. I just have no budget to put someone on such a code change that effectively reduces functionality.
Jens