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Which one seems correct?
non-xx domains (those that are not prefixed with "xx" sub-domains)
non-xx domains (those that are not prefixed by "xx" sub-domains)
I'll give this a quick answer, as it is not, as far as I can see, an exact duplicate of this question, albeit it is related.
'Prefixed by' and 'prefixed with' are used just about equally today, according to Google NGram. Either is fine, although in the past 'prefixed by' was used far more.