WordPress core does not contain obfuscated code (with unfortunate exception of revisions easter egg).
While wp-config.php can (and often does) contain arbitrary code, it is not normal for extensions to add anything there and there isn’t an API way for it. In a nutshell it is meant to be edited by hand for specific configuration purposes.
I would assume any obfuscated code in that context to be harmful and site compromised.
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