not to derail but I'm really curious:
Why not do it with a traditional language instead? is this program something that would be easily done with Construct?
Now, on topic: write a proxy program that creates a text file with the options, and read them within your construct app.
As Yaraslau said, you can then merge the .exe files, but I have no idea how.
Yaraslau if you can explain or point to a resource that does, that'd be great.