Commerce5 cannot preserve grid positions from Counterpoint when uploading products to Magento but the sort order can be manually specified from the Magento Admin. This will 

To manually specify the sort order - From the Magento Admin, navigate to Catalog > Attributes > Manage Attributes.

Select the attribute you want to modify from the attribute grid.

From the Edit Product Attribute screen, click the "Manage Label / Options" tab on the lefthand side. In the "Manage Options" section, modify the number in the position field to change the order that the values will show in a Configurable Item dropdown menu. Lower numbers will appear first on the list.

Click Save.

The specified position will reflect in the attribute dropdown.