this simply breaks in Gradle 3.1 or only when certain things are applied?

It appears not. I tested it on 3.1, 3.0 and 2.14.1 and they all ended up failing. I have a simple example project that causes the error.

plugins {
  id 'java'
  id 'com.github.johnrengelman.shadow' version '1.2.3'
}

configurations.each { configuration ->
  def upload = project.getTasks().getByName(configuration.getUploadTaskName())
  upload.repositories.ivy {
    layout 'ivy'
    url "$buildDir/repo"
  }
}

If you read the docs for RepositoryHandler it says that the mavenDeployer() is added by the maven plugin, so it probably its not accessible in this case.

If I update the example and use the local build I have (without the if(mavenPlugin) part) I still get the exception.

* What went wrong:
A problem occurred configuring root project 'tmp'.
> Could not find method mavenDeployer() for arguments [] on repository container.

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

However when I add the maven plugin specifically the build works. Given the working example, if I switch back to the public version of the plugin I again get

FAILURE: Build failed with an exception.

* What went wrong:
A problem occurred configuring root project 'tmp'.
> Could not get unknown property 'mavenDeployer' for repository container.

If I re-add the if(mavenPlugin) part of the patch and remove the apply plugin: 'maven' the build works against my local copy.

hmmm, this breaks automatic configuration of the maven plugin.

I've merged this change in the https://github.com/johnrengelman/shadow/tree/shadow_1.2.4 and then fixed it up a bit. Waiting on another report and then I'll release a 1.2.4.

Fixed by 6d18b90