I’m sure that buying a “cloned” system, there are some design changes allowed for every client. In fact, some just sell the system and it stays the same as others because it was bought by clients that had no experience in doing the work. If you later have someone who knows how to modify the files and server-side scripting content, payment gateways, etc., I’m sure you can make enough changes as to NOT be a total clone.
Google looks more for content. There’s other criteria which the Google ‘Bot looks for, but it is not concerned about the look that much. Your meta tags, descriptions and keywords will be different and other SEs still use these. If the company selling the package also has a SEO service, then you should do ok.
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