Well, generally, the telescope folk don't use encoders they count steps and do it all with dead reckoning and some compensation factors for periodic error and the like. Of course they have the stars themselves as precise points of reference.
As you've discovered reliable microstepping? is very much limited by rapid torque drop off for a given power input. Increasing the power as high as the motor can safely use and/or using a bigger more powerful overrated motor are the way forward to this.
After about x16 microsteps the additional steps are more about smoothing the motion and reducing noise/vibration than reliably precise positioning.
There's a "devestating" table somewhere showing torque drop with increased microsteps and the relationship between power input and achievable reliability.
I can find it if you like. It lets you calculate the size of motor and PSU you need to achieve the microstepping level you desire for a given torque requirement.
Some of the SSS drivers allow mode switching on the fly using the spi interface. ?
