If you do this study-ability option, you can go on to an applied university that offers a BA for a lot of degrees, although not all that 'proper' universities offer. Afterwards you can go on to an MA still.
In the entrepreneurship world, three years may be too much. But I can see a solution in figuring out a system where each company keeps each apprentice for one year, so each apprenticeship includes work at three different companies. This would allow the apprentice to get to know the world of start-ups and big companies alike, allowing him to make a differentiated decision when it comes to search for an employer afterwards.
While many companies in Switzerland will prefer a university graduate over an apprentice, I do think especially Silicon Valley would be open to look at (at that point) experienced programmers with a wide variety of start-up and enterprise experience under their belt, as well as a decent basic level of general knowledge due to the two days of school each week.
What I'm coming at is that I doubt you would have to reinvent the wheel. Look at well-organized examples of apprenticeship-systems around the world, adopt and adapt the best-fitting one, and make it work for your ecosystem. It's a great way to make more practically oriented people more valuable for society.