I don't know much about shipping (ie, fan fiction content that is usually focused on new sexual/romantic relationships between characters) but no, shipping without pedophilia is not equivalent to shipping with pedophilia - not in terms of it's 'potential for scandal,' criminality, or ethics.
I think your judgement to call out that person's pedophilia (that involves a minor IRL) was sound. Their minimization of their behaviour does not surprise me. One barometer I use for this is lemmynsfw.com's moderation policies. Underage AI content (and any kind of underage content) is forbidden. Protecting children from sexual abuse is a hard line in society, as it should be; and it's everyone's job to offer protection however they can