You don't need to do anything in software, just follow the rules ...
- The lowest bit of each byte must be aligned between the i.MX 6ULL and DDR3 chips.
For example, D0 of i.MX 6ULL to D0 of DDR chip, D8 of i.MX 6ULL to D8 of DDR3 chip.
- Other data lines free to swap within byte lane
... and the DDR controller adapts to your actual implementation.
The Note about the "DDR IC" register is not relevant here.
Regards,
Bernhard.