Only generate kythe xrefs on the primary module

Currently the kythe build is hitting the 6 hour timeout, but we're
generating kythe files for all variants. Generating them only for
the primary variant should drastically cut its runtime.

Bug: 345440993
Test: Presubmits
Change-Id: I3846b25c7f0bc22153e4f0a0cb81c5015854dd70