With a dual rad full custom loop stuffed into a true mITX case, you are preaching to the choir there brother lol. I fully understand the situation with the M.2, mines not only buried under the gpu, but also at the bottom of the stack that includes the audio daughter board. (Asus X570-I).
So, instead of pulling the loop apart, would a pcie M.2 adapter in a lower pcie 3.0 slot not work? They come in single, dual or quad layout, this would leave your loop and your OS alone on the pcie4.0 card, and adaptable/expandable storage within easy reach. Negating the possible downsides of the riser and/or cloning process and negating any possibility of leaks, changing tubing lengths etc.
Like this.