One reason the columns' order is synced is that Schema Sync should 'prepare tables for Data Sync”. For Data Sync identical columns order is mandatory as the algorithm is checksum-based. Checksum on a+b is not the same as on b+a. So we will not discard columns' order in Schema Sync. What we can consider however is an option for user to “ignore columns' order differences”.
We are in the process of finalizing the next (9.1) beta release. This one is feature frozen now. After releasing it we will return to this discussion. I cannot promise anything currently (neither IF nor WHEN we will provide this option).