Hi,
I'm not sure of the exact reason on the PT6 but it has been used on larger gas turbines to improve the turbine efficiency. By counter rotating the shafts, the turbine nozzle guide vanes between the gas generator and the power turbine have to turn the air through a smaller angle thereby improving efficiency. Most new generation engines utilise this e.g. Trent 900, GEnx and maybe the GP7000. I believe it was first introduced on the BAe Harrier Pegasus engine though.
On smaller engines it may be used to reduce the induced gyroscopic forces?
Cheers,
P2C