That’s as designed because for such configuration build system actually utilizes multiple toolchains, or at least their platform files.
In sum, you should set Target Architecture to Multiple only on packaging project in Tegra-Android Platform configuration.
Here’s a little recap:
For a library project that produces the actual dynamic libraries you need to go to the Platforms combo in VS IDE Configuration manager and add all of the platforms you are interested in building. Make those build first. When you build like that they would each get their own APK.
Now, go back to the packaging project settings for Tegra-android platform.
switch target Architecture to Multiple and specify the short names for the other platforms you want to pack in the resulting APK.
Tegra-Android build will trigger the build for these platforms and wait until it’s finished.
That’s how it works, since you needed a way to setup the platforms independently for proper per platform compiler flags, etc.