Hi mate.
Check out the "Configurator" section on EKWBs website. It allows you to select that case and then gives you a selection of options to choose from when designing your loop. It can guide you through the entire process from beginning to end even including fittings. After selecting that case it recommends a 60mm thick 360mm rad.
When "eyeballing it" it doesnt look like there will be any issue with 80mm thickness rad as there is plenty clearance.
https://www.ekwb.com/custom-loop-configurator/
Other things that come to mind is two 360 rad might be overkill. Are you going SLI/Crossfire or something?
You are definitely correct about flexible tubing vs hardline. Go flex first and then switch to hard once you've practiced some bends and you're confident but you'll always have that nightmare when switching out the motherboard.
There are so many ways to achieve a decent water loop but the basics always stay the same, waterblocks, fittings, tubing, pump, rads and res. Some people may disagree but you can put these together in almost any order with very little or no cooling consequence. Having said this you'll always want the pump drawing from the res first. this way it will never cavitate on air bubbles.
My rig goes res, pump, CPU, GPU 1, GPU 2, Rad 1, Rad 2 and back to res. Basically put priority on the way the tubing looks over order. You dont want ugly angled flexi tubes crossing long distances over components. Short and tucked away often looks best but this is all personal preference.
Good luck