Great work fuoco20!
So far I haven't been able to get WP Super-cache to touch my homepage. I set my Wordpress to "Front page displays: Your latest posts" under Settings->Reading. I tried to reset my Reading settings, but that made no difference.
I'll test commenting out those 2 lines you pointed out later tonight. However, I can't believe this has been in the code for 3 years and is not impacting other sites. In the meantime, it would be really nice if the developer would comment on this thread about what we are observing.