Attached is a file with instructions, an example spreadsheet, and results.

The process is fully achievable in the UI. With the same image structure

Default Photos: must be in every variation, including the parent.
Thumbnail: The first first of the default images is used as the eBay thumbnail

Variation Photos: Unique to an individual variation will be associated with that variant on eBay. If there are more than one variations with the same attribute (i.e. two green shirts in different sizes,  red shirts in different sizes, they should all have the photos for that attribute). 

Photos may be varied based on one attribute only - eBay restricts this.