Why are SKUs for variation parents not imported from Amazon?
When importing products from Amazon, WP-Lister for Amazon processes your inventory report and fetches additional information via the MWS API.
Unfortunately parent variations don't show up in an inventory report at all, and Amazon's API only returns public information including a parent ASIN, but not their SKU. Since the SKU can't be empty and has to be unique, WP-Lister for Amazon uses the ASIN as SKU for parent variations when it imports variable products.
Recently, Amazon seller support has confirmed that in order for the parent SKU and any other parent data to be included in a listings report, the seller must contact the feed department or listings department and request support to "ungate" the category reports within the inventory reports. This will give the seller access to the parent details in listing reports for 7 days. After 7 days, the parent data will be removed from the reports unless you request the data to be "ungated" again. Unfortunately there is no way for Amazon to permanently allow access to the parent data.
You are more than welcome to call Amazon's seller support and inquire why you are not able to fully export your data for variable products in a report without asking for this approval. Hopefully they will add a report that includes the full parent-child relationship data for variable products by default, if enough sellers complain the about the current situation.