Hi Sym,
The configuration tool does not allow that, but as a workaround, you can change
#define INST_FLEXTIMER_IC_1
and
#define INST_FLEXTIMER_PWM_1
to the same number that represents the number of the FTM module.
in peripherals_flexTimer_pwm_1.h and peripherals_flexTimer_ic_1.h
Regards,
Daniel