In my humble experience, past a certain point it's more important what kind of people you've gathered than the kind of organisational hierarchy you have in place. As I read your plan I keep coming up with ways this organisation can be abused, both by a stubborn "underling" who sours his relationships with his direct superior by going to the top floor too often, or by a manager who interferes too much with stuff he shouldn't.
It's obvious there will always be edge cases, that's not what I mean. What I mean is, firstly, that it's up to the people who have agreed on a set of rules to watch for these rules' enforcement. That should be part of the culture, ideally, but as I said this is up to the individuals. Secondly, for people both high and up the command chain to be bold enough to speak up when the rules have to be enforced, you should avoid creating conditions where someone feels/is in a dependent position. It's what you earlier described as "cowardly" - I think in large part the "keep my head down and they'll sort it out" attitude stems from people having too much on the line and trying to minimise the risk to such a degree where they become passive to the point of being useless when it comes to making decisions, including decisions which are entirely their prerogative.
How can you encourage independence both in managers and employees? IMO employees' confidence and sense of independence comes from being well paid so they have ample savings and are not wage slaves. It also comes from professional experience and pride in their own craftsmanship, which comes with the time of service. For managers, confidence comes from realistic setting of targets (whatever those targets may be with regards to the project). Instead of trying to squeeze out a promise they will cover something that will only get covered by inhuman strain, try to meet them halfway. But then again we come to the human factor - because you need well-intentioned managers who won't try to bargain too easy targets... It's an endless cycle.
