Most of the work in a large software project is coordination between all the minds involved. The more minds, the harder this task is. Large companies don't need people who can work super productively but might work on the wrong thing for weeks before surfacing again.
what's the incentive structure for mid-level managers that maximizes productivity, but doesn't have the managers whipping the staff to work harder?
Assuming larger goals on the level of "profit", sure. There's no point.
But alignment that people harp on about tends to be on specific business initiatives, or possibly KPI targets (generally tied to executive bonuses). This sort of alignment is how you get an alignment trap (where teams that are more aligned actually cost the business more and deliver less value than teams that are less aligned).
I also hypothesize that when you have systematically low productivity, the business/product no longer becomes aligned with the market. In that situation you actually don't want your employees to be 100% aligned with the business.
I suspect that the guy who invented gmail (or rather linked ads to the text), had he asked his manager would have been told "hell no, fix the javascript bug that's assigned this week - that is putting us behind target for the month"
I generally think one should measure new or increased capability as opposed to most other metrics.
How is an interesting question
The history of gmail is that it started as what Google called a 20% project. A side project the developer, Paul Buchheit, worked on with the knowledge of his managers and peers.
You can be the busiest person in the company, but, if your doing work which doesn't align with the goals of the company your contribution is either useless or in many cases is actively harmful.