Just issued a new release! This should resolve the issues you are having. I guess you are using Lightbox for your modals? It looks like it's just setting the modal backdrop to 10,000px X 10,000px which causes some issues for the tool. Really they should be using relative measurements. Anyways, if you'd like to inspect elements on the modal the process is to disable the tool, open the modal, and then enable the tool. This is because the tool blocks clicks not related to itself while it's enabled.
As far as what Axure is up to - who knows. I doubt they'd every officially support a tool like this because their current goal of the application is rapid prototyping. I believe they don't want the tool's primary purpose to be to serve as a redline / spec tool. Because of this, they've built in all sorts of cool functionality to help designs easily create fully-interactive mockups. As you've seen, it's quite hard to inspect elements while also interacting with them. This tool certainly tries its best, but there are definitely compromises. I guess there are two factors blocking a tool like this: how Axure generates HTML (which is bad), and Axure's general vision for their application.
I've linked below a demo of the screens you sent me with the updated code. Take a look and let me know if you find any other improvement opportunities!