So does the top x16 slot and the top M.2 slot interface with the CPU lanes, and by using the chipsets lanes I won't be seeing a bandwidth choke? Based on what I just quoted I will just be using the bottom slot because I don't see how the heatsink could harm anything.
Yeah, it depends. If you're pushing more than PCIe 4.0 x4 speeds through the chipset (which I believe is around 7 Gb/s) it may slow down. But that's a lot of conectivity, you're not really that likely to hit that kind of speed unless you have many highspeed USB devices (and the NVME SSD) connected and going full tilt at once. I would personally put the SSD in the top slot anyway.