1. Electric Make, a high-performance reimplementation of GNU make and ninja, has properly serialized build output logs since it was introduced in 2002 (https://electric-cloud.com/products/electricaccelerator) (disclaimer: I'm the chief architect for ElectricAccelerator, of which Electric Make is a component).
2. I published a technique on CM Crossroads you could use with GNU make 3.81 to descramble parallel build logs in 2009. The article has moved around since then but these days it seems to be found at https://www.cmcrossroads.com/article/descrambling-parallel-b....
3. The maintainers of GNU make took the concept described in that article and baked it into GNU make itself in 2013 for version 4.0 (http://git.savannah.gnu.org/cgit/make.git/tree/NEWS?h=4.0)