There is a column on dbo.Variations called "TaxCategoryId".
What does Episerver use this column for? (I don't really use it for anything in my code. Is Commerce using it for something "under the hood"?)
You are not supposed to look into database schema - it's a blackbox.
VariationContent has a property named TaxCategoryId, this can be used to set the tax categories for that variant. For example a wine might have sales tax of 12% while a strong spirit has sales tax of 25%.
If I neglect to set VariationContent.TaxCategoryId, what will it affect in Episerver? I'm assuming it would affect some tax calculation somewhere?
If you have TaxCategoryId set for a SKU, and it is added to the cart as a line item, and if you are shipping to an address that match a tax configuration, then yes, tax(es) will be calculated for your item.