When backporting JDK-8043340 we determined it's no longer possible to actually build anything universal even though universal binaries are enabled by default, causing some components to be built universal by default which is now causing issues elsewhere. This was fixed in the JDK 8 backport of JDK-8043340. We need to forward port the MACOSX_UNIVERSAL changes to JDK 9.

In short:
MACOSX_UNIVERSAL should be set to false by default, hotspot needs ALT_MACOSX_UNIVERSAL set to the same value as the core MACOSX_UNIVERSAL so hotspot is built with the same setting (no changes to hotspot itself are needed for this).