50°C is NOT causing any kind of thermal throttling. That wouldn't happen, or even BEGIN to happen, until you were hitting somewhere over 85°C, and most probably not until you got much closer to something over 90°C, as far as the CPU temps are concerned.
The VRM throttling on the other hand, who knows. Not the greatest board obviously, even for B360, which itself is obviously not the performance chipset. Not sure exactly what the VRM configuration on that board looks like but generally speaking the Gaming series boards from Gigabyte (Gaming 3, 5 and 7) typically have pretty decent VRM configurations on the Z boards. Yours has a 4+3 VRM configuration and for the stock boost profile that OUGHT to be ok.
Have you actually taken at the VRM temperatures (And whether it specifically SAYS "yes" in the thermal throttling section) by downloading HWinfo (NOT HWmonitor, or some other utility), installing it (Or running the portable version) and choosing the "sensors only" option while disabling the "summary" option and then looking at the VRM temperatures?
While obviously there are some benefits to having a Z board, I wouldn't even THINK about overclocking, at all, much less to "5Ghz" using any of the 240mm coolers out there unless you want to be religiously annoyed by the constant sound of your radiator fans. For stock operation it would be fine, and with that cooler that's exactly how I'd run it, but obviously your mileage may vary and what you do in terms of overclocking is up to you but honestly I wouldn't even bother spending the money on a Z board unless you can:
Verify for sure that there is throttling going on due to the VRMs.
And.
Unless you plan to swap that memory out for a higher speed kit, because that is where the majority of gain will come from switching to a Z board is the ability to run much faster memory kits. If you are going to stick with the 2666mhz memory kit, then it's almost pointless unless there is some other specific feature you need that you don't currently have. Even overclocking isn't going to give you much because there's not that much overhead there to begin with on the 9700k beyond what it already will boost to on most samples and any gains will definitely be dampened by that slower memory kit.