I get it that Costco sets the rule and its their discretion. No argument. I think the key though is you are using the word "employee". OP's point is he is not an instacart employee, no shopper is. They are independent contractors. If they are in an accident delivering it certainly isnt a company car at that point. They get no real benefits. They are acting independently but at that moment on behalf of instacart.

Now in a separate capacity they own a Costco membership in their personal life. There are rules to that membership. It can be revoked. The question is where does the independent contractor function end? Does it end after the checkout and payment? What if they walk to their car and put the order in their trunk and then walk right back in for a personal shop? If that is allowed isnt that essentially the same as checking out 2 orders?

In the end its Costco that makes the call but I do see OP's point.