There are two elements to consider in product systems – how you handle the data to effectively sort and manage and how the user navigates it. While your systems can support, and generally need, great deals of detail to understand the differences in products, the user generally wants a simplified way to navigate products sorting through larger categories and then filtering on different attributes.
If the items you are dealing with are common it may be possible to import taxonomy information from manufacturers or other shopping sites to give you a headstart but ultimately you will either have to create a parsing engine to try and assign items to categories based on the data you already have, or, hire someone to go through and do it. Automation is quickest but can lead to poor results while manual selection is dependant on a human and subject to their costs and potential errors.
As far as handcrafted items; usually a site will turn this into a “benefit” by openly explaining the unique nature of each item. You would want to reinforce this as a disclaimer throughout checkout to be sure people understand and of course quantify the varation (asthetic improvement vs major notable differances).
How would you response a customer who may not read the text of uniqueness, and yet expect the product as shown in one of the photograph?
Plus, for example, traders of Himalayan Quartz, do not promote their products online, because, though it is different; it cannot be re-made. A small change is likely to make a big difference in price of the product. And, it is something like that they have to maintain the stock of unique/individual products, under same name.
You explain it on the product page, you disclaim it in checkout and you mention it in the confirmation email. You educate as best you can and then, when people complain, you remind them of this, but you let them return it if they so choose. In theory your uniqueness should be small enough that it’s exciting. If not, you need to rethink how you approach the product and potentially collage / multiple grid photos to make it clear how widely the items differ.
Put your money into good service and good policies and you’ll find far better results than trying to force them into what they don’t want. Reputation rules the world.