Every time you think you're out, they pull you back in...
Can you tell if the thumb screws are touching the base plate on your system?
It's been a long time since that motherboard was in that case but I'll tell you this: I don't remember there being any flex due to the thumbscrews holding the heatsink in place coming into contact with the case. Perhaps the mobo standoffs are a hair too short? Or maybe Noctua started including slightly larger thumbscrews? (Those things are standardized but a little variation goes a long way in this case...)
If I were in your place I'd probably just put thin rubber washers on the bottom of the board to give them a mm worth of clearance. Tinker.
In my situation, that particular heatsink has never been removed from the 2500K, and it's still chugging along peacefully (I'm writing from it now.) So even if there
were a tiny bit of flex, it didn't do any long term harm over year or so that it was in the m350. YMMV.
Do you also experience the noise I'm talking about?
That heatsink is definitely audible at full speed. You're also getting the full sound of it because that case allows no natural sound dampening. It will be very quiet at idle in an OS and/or if you adjust the speed profile in your BIOS.
Also, what's your storage plan? I got lucky at the time that the CPU/heatsink location was such that the hard drive I installed did not directly interfere with airflow to the CPU. If you've got a HDD/SSD even partially blocking that air intake, the fan is going to have to work harder to keep things cool. If you've got an m.2 slot, use it, especially if it's on the top side of the board. That's just a no-brainer.
That said -- you should be fine with a 65w TDP. Use good thermal paste. Test it hard for a few days before you start using it regularly. Make sure you test by running something that maxes both the CPU and iGPU -- you might actually get your temps up to places where most people aren't comfortable -- it might even throttle. However, you'll be fine in any "normal" use case, especially the vast majority of Mame and other emulators.
The fact that you bought an i7 is the only (and admittedly super mild) criticism that I would have
if all you're planning on using this computer for is emulation. You certainly could've done with an i5. Hell, I built my wife a passively cooled i3-6100T (T-class! 35-watt TDP!) this past fall and it plays Blitz at full speed no sweat. Haven't tested that one with HLSL, but that's a hell of a CPU. Anyway, I don't know your whole situation but there ya go, two pennies.