Fix PHONY uses found by --warn_real_to_phony

Switch a use of `ndk` to the timestamp file that `ndk` depends on
itself.

Mark more module-specific rules as PHONY.

Test: diff build-aosp_arm.ninja (stripping _kati_always_build_)
Test: Turn on --warn_real_to_phony for Kati, see fewer warnings
Change-Id: I101ced4067780e38d18820f5d916596429087e49