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The Php lexer (part of the HTML lexer) sets the styling, but only has one word list (see here) which is used as you noticed for the Php words. The lexer is purely syntactic, it does not recognise semantics like function definitions, the ctags parser does that, but because there is only one wordlist available for php there is no way to pass the function list to the lexer to style those names as functions, so any setting in the theme will be unused.
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