There is nothing wrong with your setup. I think this is because of design decisions from several years before tools like git became popular. We will probably get more and more posts like this over time, I know I have posted a couple of them. I also remember that Erel did some updates recently (last two years?) which helped remove some unneeded changes to files.
It's probably not overly complicated to solve the actual problem, but it would also break backward compatibility, something I know Erel works hard to avoid.
Your best bet at this time is probably to post a wish for it.