Thanks for the [frighteningly] graphic representation of what's going on there. I know that you mentioned this in the Z97 ITX preview a few months back, and BT said they'd look at coolers when they did the board reviews. I can only see one of those boards reviewed yet, and was hoping for more info before I upgrade my test board to something newer. I was thinking about your outline designs earlier today, although I have a lovely Parvum custom ITX on the go, part of me wants a light and portable 'TJ-08 Mini' tower case about 15 litres and ready to carry to LANs.
The reason is simple. Most people use either bit coolers where the new socket position is better, or they use minimalistic coolers which have no such problem (NH-L9i). Your use case is the victim of the first group, your use case being rarer than the need for big coolers in cases like Bitfenix Prodigy. And not all top-down coolers have this problem, for example NH-L12 benefits from the new socket position.
I had wondered about this as well, thanks for the layout pics. I was looking to update my hardware in preparation for a scratch build case (asus h97i-plus, i7 4790s and m.2 ssd). I was planning on using the Samuel 17 I have spare but it looks like I'll be sticking with the smaller nh-l9i I'm using at the moment, possibly with a thicker fan.
Does this socket placement allow the installation of smaller tower coolers with front to back airflow, thinking along the lines of a Thermalright True Spirit 90 M? It looks like there is enough space. If not then the best option as always for an itx board is an AIO cooler. Dang there goes my sub 8 litre case design
I may have found a solution: Scythe Big Shuriken 2 Rev B (scan product page) The design seems to be more suitable to the itx layout of the new motherboards and is only 58mm tall.