Just to complement, I've tried many rads/projects with the XL.
Top, 40mm ideal, 45mm (Alphacool XL) may complicate things a bit depending on your motherboard's heatsinks.
Side, 40mm or 45mm in second chamber, no issues. The Alphacool is slimmer, so won't be forced against the cables of the front IO panel. The EK fits, just needs to be gently fitted.
If you plan on fitting the side rad in the main chamber, I would stay with the 40mm if you plan to install the fans in main chamber, as the 5mm difference would put it very close to the bottom rad.
Bottom, the only limitation is if you're using vertical bracket for GPU.
60mm push/pull fits easily.
The advantage of the Alphacool rads is the multiport. Depending on how you're planning to run your tubing, it can be very handy. Also, you can easily install a drain port without the need of a Y splitter.
When I was using the Alphacool rads I was using those unused ports for temperature sensors. More like a project, as I was monitoring the coolant's temperature before and after each radiator. Spoiler: loop order doesn't matter, only the air you supply to the rads.
Top rad, exhaust, side and bottom rad, intake. Yes the side and bottom will dump some heat inside the case, which will slightly affect the top rad, but most of the heat is already out the case (exhausted by the top rad), and the side and bottom rads, using cool air, will only drop the coolant's temperature, as low as possible.