Check out this answer, which shows that you can use dexTask.additionalParameters to pass additional arguments to the dx tool. An easy way to get access to the dexTask is from the variants list:
android.applicationVariants.all { variant ->
Dex dexTask = variant.dex
if (dexTask.additionalParameters == null) dex.additionalParameters = []
// This is just an example:
dexTask.additionalParameters += '--help'
// you could use others, such as '--multi-dex', or anything else that appears in the '--help' output.
}
From the source of AndroidBuilder.java, you can see which commandline arguments are already being added to the dx tool before appending your additionalParameters.