In Visual Studio 2012 onwards, the MSI project are getting replaced with Install Shield or WIX projects. I've decided to go down the WIX path because I've had bad experiences with MSI packaging tools in the past.
In the VS project world, Continua allows you to update the AssemblyInfo file, via an Action. In the WIX project world, I have the version details locked into a "Config.wxi" file. Here is the section that include the version details.
Looks like the forum is messing up your posts. From memory, wix files are xml. My recommendation would be to use FinalBuilder for this, whilst it is possible we could add an action to do this at some point in the future, it's not in our immediate plans.
I should also point out that it is FinalBuilder which is keeping the company afloat, so adding functionality that is already in FinalBuilder (which is funding both itself and Continua's development) to Continiua (which is only starting to make money, nowhere near enough to fund it's development) is a delicate balancing act.