Yes.
there isn't an easy way to do what you want, as far as I know, but it can be done. To my knowledge, Cp doesn't allow you to resize the recording area so you can't adjust it to fit within the confines of your content area in your master slides. The recording area is always the same size as your slides.
When you record slides, the 'background' of whatever you're recording (that is, the static parts) are merged into the background of the slide, and all the other 'stuff' is on top of that background (mouse, captions, highlights, etc).
If it was me, here is what I would do:
1) I'd cut out the white space of your master slide background so it's transparent.
2) I'd manipulate the application window (if that's even possible with your application) so it will fit inside the confines of my content area.
3) When recording, move the recording area box (red outline) so there is the right amount of space above, below, and beside the content area so the recording fits within the now transparent 'window' of the master slide.
Note, step 3 would probably take much trial and error to get it perfect.
4) when the recording is done, use the master slide for the recording slide. The graphics for your master slide will sit on top of the recorded background (which should only cover up either your desktop behind/around the application or parts of the application window you don't care about).
Sorry I can't upload screenshots (information security) or I'd try to help more. There may be a different/easier way, but I'm not always known for doing things the easy way. Hope that makes sense, let me know if not.
The other option is you could take a bunch of static screen shots and manually build the slides. Kind of defeats the purpose of recording with captivate, and it can be time consuming, but it could also work. I've had to do that before when we were building training for a system that wasn't built yet, we built it off mockups and wireframes from TI development and fabricated all the data with text boxes.