My question is, is this a software issue that could be fixed by someone (perhaps me) implementing the "On the Go" protocol on the Primer2 or is this not possible due to hardware issues.
The Primer2 is equipped with a STM32F103E that has a standard 'device' USB controller. The STM32F107 is pin-to-pin compatible, and it has a OTG USB controller. I don't think that you emulate OTG with an non-OTG device.