I would argue that the problematic conflation exists in the original program, insofar as the 20 under 20 program is often described as a potential replacement for higher ed. As far as I see things, there are a whole bunch of extra factors which are much more extensive than your three categories and which require a much more rigorous analysis.
For example, how do we foster innovation in specific subjects? For instance, we presumably know that with respect to atomic physics, this requires highly knowledgable people who have spent a lifetime studying very abstract subject matter, and this is most likely to be facilitated by institutions not governed by a profit motive. This is not quite as clear for innovation with respect to alternative energy, which may require any of the following: developing new types of energy, developing the technology which employs the new type of energy, or bringing an existing technology to market. The skillsets required for all of these areas are different, as is the institutional setting in which they will foster. If you take a very brilliant person who could ostensibly be working on harnessing new potential energy from the atom and put him in a program focused on entrepreneurship this would be a total mis-utilization of talent and, consequently, a huge step backwards. This is to say that business and entrepreneurship are only a solution for a certain set of problems and these are not the only problems.
Also, certain subject areas require super-specialization. So you need to start early and stay focused. The means for doing this will probably depend on what the subject area is. Is "higher ed" the solution for a would-be master electrician? No, probably some combination of vocational school and apprenticeship is. Likewise for a pianist. You go to a specialized school for a specialized subject.
Standard higher ed is an easy whipping boy insofar as it is often the default solution for many people who don't know what they want to do with their lives, many of whom don't actually end up taking advantage of the resources available to them and learning all that much. In a certain sense this might be a fault of the institutions themselves, including massive inflation in costs, multiplication of institutions, and failure to actually teach anything of value. However, the fact remains that for certain cases, there are no obvious better options than higher ed.
In any case, I think higher ed should be looked at as a set of tools rather than a solution to a specific problem, least of all the question "what should I do with the next four years of my life?" If you look at it that way, you might find that the tools that are available for you, including potentially interacting with a number of bright and diverse people and broadening your experience in various unexpected ways will be beneficial in many ways.
Case in point: I was chatting with a professor at Harvard yesterday who studied French and German before focusing on Arabic, and he was lamenting the fact that he had not had the chance to study more Sanskrit (he did study a bit) or Urdu or get his Persian up to snuff, all of which he though would have deepened his understanding and approach to life, which have some relationship to his scholarship. Of course, all of these things take time, and usually they take some form of institutional support, but as far as I see it they can be valuable if they expose you to certain ways of thinking about the world that you might not experience otherwise.
For that reason, I think you are right about entrepreneurship as a possible thing to do alongside your studies or even to replace your studies, but it very much depends on the person and where they are trying to go with their life. There are a lot of very hard problems that cannot be solved in the context of a startup and indicating to the youth that this is the best option may deprive them of valuable life experience.
As for the specific question of age, I agree that there is no set time to do anything in life. There are, however, natural patterns, insofar as people are not usually ready to leave the home and exist on their own until sometime in their late teens. What they do at that point probably should depend on their talent and proclivities. In that sense, I do think that Thiel's initiative may be right for some people. It is, nonetheless, billed as a solution for all sorts of problems for which it is not (much like the gazillion online education initiatives).