is there another issue i am missing?
No, that should work. However as already posted, using a single common emitter transistor will result in a reversal of control action. That is at 0% duty cycle in software the control voltage will be full Vin voltage output and 100% duty cycle will result in near zero voltage output. Just makes the software a little more tricky, but not that big a deal. Biggest concern is if Vin is over 10vdc then the control voltage to the ballast will also be over 10vdc, does this cause any harm to the ballast controller?