Thanks for the explanation. I now have a much better understanding of what you are trying to accomplish. And can give you a definitive answer. Of course, "definitive" to me may just be plain wrong if I missed some subtle point. With that in mind, here goes.
An iframe to a non-WordPress web page leaves WordPress and my plugin "out of the picture" in the sense that "the_content", or any of the other Filters and Hooks that WordPress provides, cannot allow my plugin to intervene and modify any part of the non-WordPress web page. The web server sends the non-WordPress web page directly to the user's browser which means that WordPress "never sees it" and therefore cannot modify its content.
As for performance, by definition, any plugin adds code, which normally reduces performance. The only exception is performance-enhancing plugins that change how WordPress does something, improving its performance more than the plugin reduces it.
There is no meaningful way to quantitatively measure plugin performance because each web server has a different set of processors, which varies the amount of processor time each php statement takes to run. The other factor is network traffic to the user's web browser. That can be measured, but performance is about time, and network speeds vary from one web server to the next, based on its connection speed to the Internet and how much other traffic is sharing it, and on the user's connection to the Internet.
All that said, I have never detected any measurable slowdown when using my plugin. I've tried to be careful in my coding (I began programming in 1971), but with the large number of settings I've added over the years, plus support for specific plugins and themes that happens behind the scenes, there is a fair amount of PHP code executed for each page displayed.
Back to your design problem: if you want to stick with your current approach, I think you have to either have a cloned copy of your non-WordPress pages with all the links corrected. Or write your own PHP code (as a custom plugin just for your site) that replaces the iframe with a WordPress solution that actually inserts the non-WordPress web page into a WordPress page, modifying it during that insert process.
