Brainstorm here - could you put a number of lower resolution encoders firmly on the same shaft? The theory would be they'll all pulse on slightly different but consistent phases.
Simple example, an encoder is capable of 60 degree resolution. I'll mount 5 of these which will all have some variation in phase, and I'd average out to having 12 degree resolution, with variation that could be modeled statistically.
Conceptually I would have a shaft with n different key slots, one per encoder. This would ensure there will be variation as opposed to having the phase be super similar, such as +/-1 degree in the above low resolution example.