Well I haven't downloaded or played with it. I can think of 1 easy way it could be done.

Two apps.
1. Simply create an application that will be able to read the end of its exe. At the end is a link to the file to be displayed/opened or possibly the entire file simply appended onto the exe. When the app is double clicked/opened up, it knows what to do with the stuff appended to the end of it. You can search for self-modifying executables on this site and elsewhere for examples.

2. Your "branding" app has in its resource file the app in #1 above. When you click a file to brand, you basically copy the app in #1 out of your resource file and append the target file to the end of it.

That's about all I can give you. This isn't my cup of tea and honestly not that interested.

As for building an actual exe on the fly, forget about it unless you create and deploy your own compiler.