I have answered these questions via email. I’ll post them here in case anyone has a similar problem:
Would storing the Meta Box data in a separate db table keep the relationship with each product ID it was entered on
The answer for this is YES. There’s a relationship between the products (posts table) and the custom table. Technically, the value of the custom table’s ID column = product (post) ID.
Whats the best approach to something like this?
If what you meant is exporting the data in the custom table when using the export functionality of WordPress, then I have to say it’s not supported. WP export feature seems to be limited to custom fields that stored in the
post_meta table only.
I have no good solution for this at the moment, as the task of exporting and importing data from custom table along with the product data seems to be complicated. It’s best to use some tools or plugins to export the whole database to SQL file. But I guess it’s not what you want.