I ran into this problem today as well, and searched through git to see if there was a recent fix. I found a commit on the chaos branch:
The commit adds the following to the end of the HeadlessChaosTarget constructor in HeadlessChaos.Target.cs
// Force enable Chaos as the physics engine for this project as this
// is a Chaos unit test framework - it doesn't build with PhysX enabled
bUseChaos = true;
bCompileChaos = true;
bCompilePhysX = false;
bCompileAPEX = false;
bCompileNvCloth = false;
After adding those lines I was able to compile my project without having to add Chaos to the engine target.