Is this a really low end motherboard? Are all your case standoffs installed properly?
This will cause early trace failures for sure, possibly other things. I would suggest that if the cooler is this heavy you probably need to consider putting something far lighter, or stock cooler if your CPU can operate that way. Lots guessing without knowing what this hardware is.
If you can't change the base hardware, like a thicker PCB mobo, an AIO cooler plate might be light enough to eliminate the board sag.
Early on in my PC building and modding I had come across a really nice ThermalTake tower cooler that was entirely copper and heavy as could be. In retrospect, completely unnecessary for the builds I was messing with. I ended up putting it on either an H or B chipset value board and not long started having strange issues with USB, memory, other assorted glitches and BSOD until one day it just didn't work. It wasn't until much later that I gained the knowledge to realize what had actually happened.
That cooler is actually still in use at an acquaintance's house on an ancient AMD.
There may be something interfering that makes the board warp as you tighten down on the screws. t might help to isolate the cause of the warpage, first is to take the cooler off the mount and check. If the warp remains then you know it's not the weight of the cooler. Then loosen the mount to backplate fasteners.
Also, could cooler parts be interfering with the VRM heatsink that's closeby? When you remove it from the mount you'll see the warp relaxing if it is.
So I removed everything on the motherboard and this is still how it looks like without anything on it, it still looks to havet that small bend still, also compare to picture below when its not in the case, looks the same to me? So the CPU cooler wasnt bending it after all and it just looks like that.
Even if it's not the LGA1700 ILM doing it could be the AK400 cooler mounting bracket and backplate. It appears that should those four wings where the mounting studs are located on the backplate not be perfectly co-planar with the surface underneath the CPU socket it could impose a bending moment that warps the board. Loosen the mounting screws for the topside CPU cooler mounting frame to see if that's the case.
I removed everything and screwed everything back on, including removing and putting back the backplate.
I/O panel is on now as well, and taking off and putting on the case standoffs.
Looks good enough to me now I guess.