I will discuss the issue with the Automake maintainer. I have never used Automake myself, so I don't know the issues.
One fact I can see is that this is just a matter of defaults, and doesn't stop users from doing whatever they want. Please don't exaggerate. Making Automake have different defaults on different platforms is clearly a bad idea. If you are annoyed about one consistent default, inconsistent defaults would be far more annoying. However, some other change might be an improvement.
