I think it’s a combination of many factors. First, they kinda merged a lot of the characters from the novel into a few key persons. Little Meg and Little Jammes seems to have been combined, as has Raoul/Philippe, Madame Giry/Gabriel etc. From there they went a bit freer on creating these character’s looks. Madame Giry is not the tacky mess Leroux describe, for example.
Second, they based Christine partly on Mary Philbin’s dark curly look, and partly on Sarah Brightman’s own look. So she became a curly brunette, though described as blond and blue eyed in the novel.
To contrast brunette Christine, they made MEG the “blonde and blue eyed” character. Though Christine is usually not featured with darker skin, it’s like they swapped the appearance of Meg and Christine. Though in West End they’ve just swapped it back, haha.
There might be further aspects to this, but I think that’s basically how it went down.