The same definition would be a problem in Android.mk too -- in fact, this warning is coming from the makefile system (since the makefile system still handles installation for both Make and Soong).
It looks like inside Google, we're not defining `prebuilt_etc` or `BUILD_PREBUILT` definitions for this file, instead we're installing it via PRODUCT_COPY_FILES in your product configuration. That way every product can choose how to install that file.
Or you could "hide" one of the modules from Make using soong namespaces, only turning on the one that you want for a particular device. Then make will only create a single installation rule. (I haven't tried it, but it should work -- this is how we handle more complicated modules that need to be different per device)
- Dan