Yet another possibility for this is the ZenCart was based on the OsCommerce code (which also has the two config files) so the *real* reason for it is unknown to the ZenCart developers, but since it has several potential benefits there has never been a need/reason to adopt a single config file system.
Also just a FYI, the code(s) you posted earlier both worked fine on my test DB running MySQL V5.5.38.
I do/also suspect that the issue is somehow related to MySQL versions though.
Cheers
RodG



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