I could be completely wrong, but it seems if you can not make the 60% at your destination you may still depart for your destination provided you have an alternate planned that meets all the requirements for the paragraph.
I don't think that defeats the 60% rule, I kind of see this as a back up lets say you lose a system ex. some of your hydraulics and this might prevent you from landing with your Flaps extended requiring more runway.
If the 60% rule wasn't there you are in the middle of nowhere with no reserve fuel and you do not have enough runway to make a safe landing. (e) allows you to go to the airport of choice if all your systems are working. But if something were to fail you still have the alternate fuel required to get to an airport that would allow for a safe landing.
Just my take I've never had to deal with 135 stuff though, I'll be watching this topic to see other opinions.