Merging project files would be a nightmare, since every game will be using its own object types, its own event sheets, etc. So no, anything is better than this solution, even with your python program I don't see how this would be practical.
Since construct apps are just a canvas on a webpage, the iframe solution is great. You can create a javascript app that would run/stop your games.
If you need the games to communicate with each other or with the main app, a solution is to have a server with which the games communicate using AJAX. I worked on a project where I did just that, except I didn't use AJAX (async- javascript and xml) but rather AJAJ (async javascript and json).
Inside Construct you would need a custom addon that exposes the API of the server in the form of actions, expressions and conditions. You can require the people who are making the games to implement your addon in order for their games to access your platform's features.
Basically, you're making a game portal, just like Scirra Arcade. However, with some careful planning and javascript-jutsu, you can have everything in a local server and have smooth transitions between the games to make it look like a giant uber game to rule them all and in the darkness bind them!