Apparently this is a known bug in the SDK. The solution was to switch the component to flexCAN and write this in the FLEXCAN_DRV_Init function:
if(((base->MCR & CAN_MCR_MDIS_MASK) >> CAN_MCR_MDIS_SHIFT) == 0U)
{
/* To enter Disable Mode requires FreezMode first */
FLEXCAN_EnterFreezeMode(base);
FLEXCAN_Disable(base);
}
#if FEATURE_CAN_HAS_PE_CLKSRC_SELECT
/* Select a source clock for the FlexCAN engine */
FLEXCAN_SelectClock(base, data->pe_clock);
#endif
The idea is it check first if the module is already in disabled mode as expected to be the peripheral after reset and if is not already disabled then to force the freeze mode and disable the CAN module.
This workaround, at this time, is not possible using the can_pal component.