Your right to a certain extent. The lightbox content would not be attributed to the landing page directly but it would still be crawled (as long as you’ve not ticked the boxes to “hide from search engines”) however I believe that only the content found on the landing page itself is used to determine relevance and impact on the page quality score.
While that might make you think lightboxes are not as good as they first look please don’t jump away from them just quite yet. The benefit they give to user experience and feel of a landing page quite often has a noticeable impact on conversion rates, if you’re getting more conversions but a slightly lower quality score isn’t that better for business?
Now my top tip to combat this… FAQ’s at the bottom of your LP. Style them so they are grey, plain and boring and don’t pull any attention away from your main LP message and form. Keep them smaller and at the bottom of the page but use them to add content to your LP for the purposes of increasing relevancy and quality score. Don’t try to hide them with CSS tricks (hidden content is often marked down in its value slightly for SEO so I believe from our tests this is also the case for LP content in Adwords quality score).
Well written FAQ’s on the bottom of a landing page can really help your quality score if that’s what you’re after, but my recommendation, don’t chase quality score too hard that you sacrifice optimisation for conversions, chase conversions more.
I hope that puts a bit more light on the situation and one of many possible options,
Best of luck and feel free to shout out any more questions if you have them.