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@ Monty
I agree in essence with what you are saying regarding separate logins, however with back up a SSL and a note explaining (for the noobs), then security would be shown anyway.
The reason why most want a shop integrated is the ease of use and convenience for members, there's nothing worse than having to sign up 2 or more times to a site.
I see your point especially with storing credit card info on file, however I think the majority or at least the smaller companies (less secure maybe?) would use something like paypal, nochex, secpay, worldpay, etc, etc, where them companies take payment, hence no need for a site owner to store critical information from customers, as it done and process by that third party, but still theres the issue of 'Data Protection', and why security is needed.
Of course this is only my opinion.