I am not expert enough to say how each theme interacts with products, yoast, and CSV import. I am using Canvas (latest version) and WooCommerce.
When I do the export I also tick the box include hidden meta data (but this seems to be the meta data for WooCommerce.
I've not (so far) had the problem of the import values not showing up - but my values have always been changes to fields for existing products - I've not created a product from the CSV import since I activated Yoast. (I did use CSV to create products before I put Yoast live).
When I export my product file - I've been using excel to be able to easily change values in the Yoast fields then re-import to my site - iRedCord.com
I have one more value in the Yoast fields than they gave you, but this field is always blank and I don't use it - the focus key word value:
meta:_yoast_wpseo_focuskw (column AM)
meta:_yoast_wpseo_title (column AN)
meta:_yoast_wpseo_metadesc (column AO)
meta:_yoast_wpseo_metakeywords (column AP)
If I understand you correctly - you are finding your values in the database but within your theme you are not seeing the values populated? seems like their is an issue between your theme - yoast - csv import. I am sorry but I can't debug what is occurring for you.