I honestly can’t think of a reason why the unanimous (!) staff recommendation would get overruled besides ideological opposition to the Voting Rights Act or a desire to see more Republicans in Congress. If anybody out there can think of better justifications, drop me a line; I’m all ears.
Perhaps the staff of the Civil Rights Division has been enforcing an interpretation of the Voting Rights Act that goes beyond the statutory requirements of Congress, and therefore has been making recommendations that do not enforce the VRA but implement something more stringent than the VRA. Thus, the political appointees at the agency felt an obligation to limit the review to the bounds of the statute, rather than the imagined law that the Civil Rights Division staff would like to see implemented. For example, the memo complains about partisan gerrymandering, yet partisan gerrymanders are not illegal under either the VRA or Supreme Court precedent (even if they probably ought to be).
After all, it is not beyond the realm of reason that young, bright attorneys might choose to join the Justice Department’s Civil Rights Division, and forego greater earning potential and prestige in the private sector, for ideological reasons.