UCD3138: can PWM0A and PWM0B waveform be swapped?

I assume you mean DPWM0A and DPWM0B.  If that is the case, the answer is yes. 

Just put a 3 in THE PWM_A_INTRA_MUX and PWM_B_INTRA_MUX bitfields in the DPWMCTRL0 register.  You can move things around a lot with those registers. 

For real fun, try the edgegen registers. 

Note that when you do this, you lose the high resolution dead time calculations.  It goes to 4 nanoseconds, instead of 250 picoseconds.  Not generally a big issue on isolated power supplies.