Here are the results based on the quick study that I did.
For the coded experiment:
wing_length will be -0.6 and 0.6 for 3 and 6 respectively for both Case-1 and Case-2
For Case-1, base_length will be 0.25 and -0.4 for 5 and 3.5 respectively.
For Case-2, base_length will be 0.33 and -0.33 for 5 and 3.5 respectively
We can see that Case-2 has results very close to Case-3 which are based on the actual factor values. It should also be noted that the base_length has a very small effect on the prediction and hence the effect on the results is not that significant. If the same case would have been for Wing_length than the results would have differed a lot between Case-1 and Case-2
Conclusion:
We should try to choose the factor level such that the middle factor level is at exact center if it can not be done than put the middle factor level as the ratio based on the extreme values.
e.g. in my case of base_length, since the middle factor level cannot be put in exact center if I use the coded units then I should put the 4.5 as 0.11 and not 0.