When I saw this before my guess was because the iframe called content from a different domain.
Oops, my fault for not clarifying. The content hosted within the iFrame is the site's own original content. The use of the iFrame and the 3rd party technology is purely for managing the content to tie even more robustly with the context of the keyword and user query. It should, theoretically, help Quality Score due to this... but I don't know if the iFrame or manner in which the content is served is a hindrance in this model.
...aren't there better ways of displaying this customised content than using an iframe?
Well, that's a different question. :) In order to weigh the benefits/risks, I'm trying to vet the specific downsides of this particular approach.
The short reason is that the third-party company's technology is what is managing which customized sections of content to show - so, it's preferred that the controls lie on their end...