Example:
You will never do that again and I underline never!
Probably "and I mean it" is used this way.
As you surmise, the usage is metaphorical, suggesting that if it were written, it would be emphasized with an underline. Verbalizing punctuation or other mechanics is not uncommon in informal speech.
You will never do that again, period [full stop]!
You will capital-N never do that again!
You will never do that again, dot dot dot, never!
You are brilliant. Absolutely brilliant idiomatic usage of language. However, when writing it I would write it either as
You will never do that again and I underline never!
Or,
You will never do that again and I underline "never"!
When spoken, it would reinforce comprehension to do a brief Harlem shake when enunciating the word "never".
Or, provide a more executive feel, by doing the traditional quotation marks finger gestures for the word "never".
Or, say the sentence in a more stuffy way
You will never do that again and I underline quote-unquote never!