The "solution" I finally went with does not actually resolve the fact that the section seems to be overwritten, but rather puts a bit of duct tape on it...
I implemented a wizard which I added to the template. In the implementation, I put code in the RunFinished
method which opens the project file as a xml document, and simply replaces the section with what I want it to be. It sort of works, the only real drawback is that it will alert you that the project has been changed and needs to be reloaded as soon as it is added.