I think Valve's flat structure strategy has mildly failed and they should try something else. Unless they still desire to all-in on the strategy of creating products and hoping to land a another billion dollar baby, then sure, this strategy is good for that. However Valve kind of advertises itself as a video game company, and if someone is interested in making video games I feel like they'd actually be a bit disappointed after a while of working at Valve, simply because it seems so unlikely for them to actually ever release a video game.
And the bonus structure that I recall also seems dated. iirc it was setup in a way such that delivering new projects would land you a bonus. But this incentivizes creating things, but there is no incentive to continue supporting or updating or iterating on it. In my opinion the bonus structure should be done in such a way so that if you deliver something new, you would land a bonus, and then you'd get larger bonuses at the 1 year mark, 2 year mark, etc, if that thing has been updated and improved.
Many things these days are not just a single product that you release and that's that. They continually live on, they're a service, they're interacted with for years. Valve has fallen behind in this regard. Even smaller things like mini-features in Dota 2 for example would be released, which likely earned someone a small bonus, then left by the wayside to fall apart.
I love Valve conceptually but I really wish they'd iterate on their company design instead of thinking they've "solved it" I guess. I wish they were more video game focused. Obviously I don't know how it actually is in there these days, but things like this manual and other hearsay / rumors are the best I have to go off of.
From a purely financial perspective, they SHOULD continue to focus on marketplace dominance via STEAM. Whatever game is made for HL3/TF3 will ultimately fail to meet fan expectations (Duke Nukem anyone?).