Hello,
the operation mode (burst mode, pulse-skipping, spread-spectrum) is selected via the Sync pin. Is the state of this pin only sampled during startup or can one change the operation mode on-the-fly?
To enter enable spread-spectrum mode a voltage of 2.9 - 4.2 V is needed. If the mode can be set continuously, a voltage divider on the LTM8063 output could supply this voltage.