Inplace upgrade is the recommended method of upgrading as this is the method that is heavily tested within Adobe. There are many tasks that are performed during an inlace upgrade that would not be performed if you were to use only crx2oak, for example a number of post upgrade tasks that are only run during an inlace upgrade. An example of such a task would be changes to the MSM/Livecopy, if you simply used crx2oak the content would not be updated to reflect the changes required for 6.2.
If you were to use crx2oak, then after your migration, you would need to run a full set of regression tests and then determine if the issue is a custom application issue or if it is caused by you not doing an inlace upgrade.
Regards,
Opkar