Chet Hosey wrote a nice explanation here:
Historically, Ant always included its own runtime in the classpath made available to the javac task. So any libraries included with Ant, and any libraries available to ant, are automatically in your build's classpath whether you like it or not.
It was decided that this probably wasn't what most people wanted. So now there's an option for it.
If you choose "true" (for includeantruntime), then at least you know that your build classpath will include the Ant runtime. If you choose "false" then you are accepting the fact that the build behavior will change between older versions and 1.8+.
As annoyed as you are to see this warning, you'd be even less happy if your builds broke entirely. Keeping this default behavior allows unmodified build files to work consistently between versions of Ant.