Your stage 2 build also has --bootstrapping=off? Maybe it's getting overridden internally because of the presence of the stage 1 build, in which case, better not add that flag if only because it's confusing.
I've been seeing this lately when cross-compiling the Swift compiler for Android using lld from the Android NDK, worked around it here. I haven't looked into why it happens, likely tied to the lld version.