And how are the Rebels going to operate those droid starfighters? They'd need control ships. That, and the Empire is, given the Clone Wars, very good at fighting droids, especially with 19 year old combat algorithms (ie: the same ones the Empire fought in the Clone Wars).
The Empire used ARCs (along with V-wings) in its early days so in their Imperial colours they're just about justified there. But putting them in other factions would be shoehorning them.
The rebels in tarkin had control ships so it's in cannon they can get access to separatist ships.