Android Studio 2.4 Preview 4
Build #AI-171.3870562, built on April 1, 2017
JRE: 1.8.0_112-release-b736 x86_64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o

gradle-3.4.1
classpath 'com.android.tools.build:gradle:2.4.0-alpha4'
buildTools : '25.0.1',
compileSdk : 25,
javaVersion: JavaVersion.VERSION_1_8,
minSdk : 16,
targetSdk : 25

Multidex is setup and works fine (compile, assemble and espresso test) with:
classpath 'com.android.tools.build:gradle:2.3.0'

When we bump up to 2.4 alpha 4 we get multidex issue when we try to run the tests:
(I repeat multidex is setup properly and everything works fine on plugin 2.3.0)

This is a scaffold-like very close to our project setup that I created to reproduce various gradle issues we encounter with our enteprise project:
https://github.com/originx/Gradle_troubles_android_enteprise
(sadly I did not update it and maintain it in some time I can refresh it if you really need it or feel free to fork or PR)

This is the stacktrace of the issue
https://gist.github.com/originx/c79f75517b7b2cef09e8c8904086eee4

This is the command I ran on our project (should be the same on example project I attached)
./gradlew clean connectedNonpayUnitedStatesBleedingDebugAndroidTest --stacktrace

but I repeat I do not know yet does that project compiles even with the new plugin I can update it later on if you need it.