I am the tech lead @Google for the Android Gradle Plugin, let me try to answer your question assuming I understand your use case.
First, some users mentioned you should not share your InstantRun enabled build and they are correct. The Instant Run builds on an application is highly customized for the current device/emulator image you are deploying to. So basically, say you generate an IR enabled build of your app for a particular device running 21, it will fail miserably if you try to use those exact same APKs on say a device running 23. I can go into much deeper explanation if necessary but suffice to say that we generate byte codes customized on the APIs found in android.jar (which is of course version specific).
So I do not think that sharing those APKs make sense, you should either use a IR disabled build or a release build.
Now for some details, each slice APK contains 1+ dex file(s), so in theory, nothing prevents you from unziping all those slice APKs, take all the dex files and stuff them back into the base.apk/rezip/resign and it should just work. However, it will still be an IR enabled application so it will start the small server to listen to IDE requests, etc, etc… I cannot imagine a good reason for doing this.
Hope this helps.