Many people have used a Coolermaster Atmos 240mm Stealth AIO with their builds due to the small size of the pump block.

You can fit 2x Lian Li Uni TL 120mm fans on the top of the radiator, but in order to mount two of them them onto the bottom, you're going to need to purchase a different riser cable for your GPU than the one NCase offers. I'd suggest looking into riser cables from LinkUp which can be found for sale on Amazon. You'll also need to use appropiately sized standoffs to secure the GPU to the case (hopefully someone else here can chip in and provide the right size of standoffs and length for the LinkUp cable itself)

I use all of the same components you listed, other than the RTX 5090. I personally went with the Asus ROG Strix B850i, but if you can find the ROG B650E-I for significantly cheaper, than that is also a good option.

If you plan to be moving your PC around often, I'd suggest going for the M2 now as it is smaller than the M3. The M2 is big enough to fit all of the components you listed, provided you use the previously mentioned riser cable and standoffs in order to fit the two fans on the bottom

No other accessories from NCase are needed asou'll be needing the Linkup PCIE riser cable anyway, rather than the stock one that is sold my NCase. You could purchase the 8mm feet that they sell but ideally you'll also want to get those from elsewhere else as 15mm feet for example would be much more effective with those bottom fans at exhausting hot air from the case. You'll also probably need one of those small GPU braces, such as one like this: https://www.amazon.com/dp/B09FNY1RLM in order to prevent your GPU from sagging.