I will leave it here in case it helps someone. I am using the following style in my geany.css:

#geany-compiler-error {
    color: #FF7987;
}

#geany-compiler-message {
    color: #DFDBFF;
}

#geany-compiler-context {
    color: #FEC0E0;
}

It has been easy to read the compiler messages on the dark themes I tested it with.

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