I understand that this option in my build.gradle file is what I seek.
android { dexOptions { incremental true } ...
Glorious incremental build. However, this doesn't work for me apparently because my project uses the multidex feature for retrocompatibility with android versions before Lollipop.
Proguard to the rescue! With Proguard I am able to minify my executable and remove all the unused methods. I got a couple of errors with proguard minify but was able to set it properly and get it working. Great! Dex generation takes about 20s for every build. Unfortunately, nothing is for free, and the proguard gradle task takes about 2m50s to run. Even worse than my initial case.