The two times I've had in-store card referrals (high value transactions: the first time was buying a P3 laptop, which was quite high end in those days; the second was furnishing a new apartment after moving to Houston), I'm pretty sure it was the issuing bank ultimately handling the call - I can't imagine the bank would have transferred the personal information they were asking for as a security check to the merchant services provider: past unlisted contact details, previous transactions etc. I suspect the call may have been transferred to them, though, rather than called directly.
I had a similar issue this year with British Telecom working on a broadband fault. The service manager wanted to speak directly to the field engineer working on the fault (different divisions: the engineer's BT Openreach, the manager was BT Wholesale) - but the Openreach guy said he couldn't call the Wholesale one directly. So, the Wholesale one called my number and asked to speak to him