I can easily see why IFRAME content isn't included in the Word document. Especially if the IFRAME is pointing to content that isn't part of the project proper.
About the only workaround I can think of is to copy the topic that appears in the IFRAME to the actual project before you create your Word/PDF output. You could condition them out for other builds.
One other thing I would really stress and encourage you should do is to report this as a need to Adobe. I'm not sure which version of RoboHelp you are using, but RoboHelp HTML 8 introduces a feature called the Resource Manager. What seriously needs to happen is to have the ability to store topics in common locations and have the Resource Manager as a means to keep them synchronized. (Link to the Wish Form is in my sig) It's my opinion that Adobe simply isn't understanding how helpful something like this could be.
Helpful and Handy Links
Had the same problem in a project. I applied a tag to the iFrame so that it only appears online. In printed documentation text is substituted explaining that in the online version whatever will be shown. Obviously that text is also tagged so it does not appear in the online help.
See www.grainge.org for RoboHelp and Authoring tips