Yes its the lexer, https://github.com/geany/geany/blob/master/scintilla/lexers/LexLaTeX.cxx#L268 which says any [ after (optional) whitespace is the start of options.

I assume latex itself gets around it because it knows the \in is a no-argument command, but the lexer won't know that, its purely syntax only, so I'm not sure how it can do anything different to what it is doing.

You could try reporting it to Scintilla anyway.

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