STR:
0. Substitute gradle mainTemplate with one provided by user at..\Editor\Editor\Data\PlaybackEngines\AndroidPlayer\Tools\GradleTemplates\mainTemplate.gradle
1. Open empty project in Unity
2. Build it with Internal builder and with gradle builder
3. Extract from both apks dex files
4. Convert these dexs to jars
5. Examine jars with Java Decompiler and see that in case of gradle build dex some classes in com.unity3d.player are missed

This happened bcs of incorrect ProGuard in Unity:
-keep class bitter.jnibridge.* { *; }
-keep class com.unity3d.* { *; }
-keep class org.fmod.* { *; }

It should be (notice the difference in com.unity3d.player):

-keep class bitter.jnibridge.* { *; }
-keep class com.unity3d.*player*.* { *; }
-keep class org.fmod.* { *; }