FOC electrical angle offset calculation with absolute encoder
I experimented with a number of different offset calibration ideas while building out my FOC system. The method I started with is the method you described, locking the motor electrical angle with an inverse park transform and comparing it against my encoder angle. I quickly moved away from this technique because it is wildly inconsistent. It's easy to show why; request a fixed electrical angle via inverse park, plot out your encoder angle, and introduce mechanical disturbances to your rotor. It will settle to a slightly different angle every time, due to real-world effects (friction, cogging torque). 

Based on experience, your observation that the motor 'spins better' in one direction vs. the other almost certainly comes from a bad estimate of the offset angle. You should be able to tweak your offset value and observe consistent torque in both motor directions.