You're right. This is also a problem with Eclipse over the IntelliJ toolchain, in general.
Eclipse has it's own compiler and it uses that to build from within the IDE. Since this is not using Javac, it means that you might and very likely will not have equivalent binaries. Not specific to Android, but this also meant that when a new version of Java is released, IntelliJ can immediately take advantage, but you will be stuck waiting on Eclipse (and NetBeans).
Personally, I prefer the IntrlliJ approach since the IDE, javac on my workstation, and javac on the build server can output identical binaries, I trust the results even more so.
My understanding has always been that you can have Eclipse invoke an external build. However, if you use its compiler you do get quite a few niceties. Largest being that it can let you debug partially broken code. (You just can't call a method that was unable to compile.)
Also, if I am not mistaken, IDEA has its own compiler, as well. It just doesn't emit bytecode.
Eclipse has it's own compiler and it uses that to build from within the IDE. Since this is not using Javac, it means that you might and very likely will not have equivalent binaries. Not specific to Android, but this also meant that when a new version of Java is released, IntelliJ can immediately take advantage, but you will be stuck waiting on Eclipse (and NetBeans).
Personally, I prefer the IntrlliJ approach since the IDE, javac on my workstation, and javac on the build server can output identical binaries, I trust the results even more so.