The real change and balance that can be done in terms of engineering is to keep communications lines open and teams relatively small as possible to get the job done (also to improve internal communication). Paperwork that is done should be focused on documentation so lessons learned in the past aren't forgotten. In other words, more of a documentation for an archive of review rather than to give meaningless numbers to bean counters.

If a rocket blows up nobody gives a damn that it took 50k man-hours to build and design. They do care about an improperly designed turbopump shaft that was off-balance where the calculations on the positioning of some parts was fortunately documented in an engineering archive (to give an example). It takes a very strong engineering manager and support from upper management to make sure that the documentation (including the ugly weekly/monthly progress reports if you work at a company insisting upon them) stays on topic and to get rid of as much bean counting type stuff (like keeping track of how much paper gets used by engineers in the printer) at a minimum.

In fact, if you have management insisting on that bean counting type stuff where they are worried about hours, wasted labor, and foolishly spent money in general, that is a strong sign that the engineering team is too large and improperly managed. If those managing the engineers can't identify by name and have strong knowledge of the work habits, abilities, strengths, and weaknesses of each engineer in intimate detail, they have let their department get way out of control and are doing something seriously wrong. I'm talking those managing engineers reporting directly to the CEO, if not the CEO himself.

SpaceX has a bit of a problem right now as it is growing so fast that maintaining those communication channels in their engineering team is becoming more of a problem. An even larger problem is that sometimes the qualities that make somebody a good engineer aren't always the same as what makes a good engineering manager, even though unfortunately you need to make some engineers in charge from time to time (and bringing in somebody who doesn't know engineering is a huge mistake in that situation). Continuing education, like even taking an experienced engineer and sending them back to school to earn an MBA or at least some decent professional management training can help (even if it is internal to the department). That can help develop the kind of culture that you want to promote too, which is one way that the military even helps to grow their noncoms to be competent... if you want to find an organization that is at least successful doing that kind of thing.