Attiny861 ATTinyCore can't use pin13 and pin12 at the same time

Yes that is correct. This is because the Attinys 261, 461, 861 are specially designed to control 3-phase BLDC motors. There are 2 more pin pairs that also run Gogen-phase, but can be synchronized to PWM. You have to look up which pins are exactly in the data sheet.