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The following code calls the correct methods with Gradle 3.3. I am going to close the issue.

def myExt = extensions.create('myExt', MyExtension)

task callExtMethods {
    doLast {
        myExt.foo "14"
        myExt.foo 14
        myExt.foo = "14"
        myExt.foo = 14
    }
}

class MyExtension {
    def foo(int a) {
        println 'foo(int)'
    }
    def foo(String a) {
        println 'foo(String)'
    }
    def setFoo(int a) {
        println 'setFoo(int)'
    }
    def setFoo(String a) {
        println 'setFoo(String)'
    }
}

The output:

$ gradle callExtMethods
:callExtMethods
foo(String)
foo(int)
setFoo(String)
setFoo(int)

BUILD SUCCESSFUL