Correctly handle intrinsics when not precompiling the boot image.

JIT zygote will mark methods from the apex as precompiled, and these can
be intrinsics. Given the flags conflict, just don't mark intrinsics as
precompiled.

Test: boot JIT zygote with primary boot image not precompiled
Change-Id: I9edba04e586befd842a7623f2f0ae3a5ac7109f6