SOLUTION

I managed to find a work around for this issue, any other medal users having this problem do the following:

1. Turn on experimental mode in the medal client.
2. Turn on experimental window capturing.
3. Add an unsupported game and now you will see the bootstrapper for MW3 in the drop down menu.

Clicking that just says there are no games running:

https://i.gyazo.com/4cff09aa452646c2a2380e28c05418e6.mp4

I have been talking to medal about it also so I will let you know if they make a fix for this, just strange that it isn't shown as a game.

Medal will not show MW3 as a listed game when trying to add an unsupported game to record.

I have tried making the game windowed, borderless, fullscreen.

I have tried making medal capture the plutonium launcher, which works actually but obviously I want to capture the game not the launcher.

Below is a .gif showing the issue.

https://i.gyazo.com/161935d7241f9434ab252c1bf485b255.mp4