You rarely see a do for emphasis in a that-subjunctive, though you see do not for negation of course. However, it's not that it's rare that makes it wrong in this case.
Speakers of different dialects will, firstly, argue whether it should be do or does, depending on whether you consider corporations grammatically singular or plural for the purpose of conjugating verbs. However, that ultimately doesn't matter either.
Consider:
It is clear that we do find examples of 'poor', non-standard written English from major publishers.
Here is a that-subjunctive emphasised with do. It is conjugated correctly for the pronoun we. It seems weird in isolation, but it would come after a suggestion that major publishers only publish 'good', standard English - but we do find examples, so that can't be true.
The difference here is that we do (or can) find those examples now. In your example, it's not something that is even hypothetically happening now. It's something that may be happening in the future. Thus, an emphatic auxiliary verb is harder to find. However, you can emphasise the effect with a semantic difference, by saying:
The country demanded that Boeing must pay a $1 billion penalty...
This is clunky, awkward language, but it provides emphasis. If you really must have the emphasis, this is an option.
You could also emphasise it by using an alternative verb from pay, though most of the options are colloquial and may be dialect specific. For example, fork over, stump up, or pay out.
What would be most appropriate depends on context, audience, and why you want to emphasise pay.
