It's not your case choice. That's a very decent case and really no different in design than many others.
It's air cooler design combined with physical limitations. Which is totally out of your hands.
I once bought a Raijintek Nemesis. Excellent cooler, on par with the NH-D15 or Cryorig R1 Ultimate. Tickled pink that it was on sale and I got it for $40. Went to install it, didn't fit. The VRM heatsink on my MSI mpower is massive, sticks up very high. The pipes on the back/underside of the cooler hit the heatsink, so it wouldn't seat right. That's a design flaw not considered when the cooler was designed.
Now I own a Cryorig R1 Ultimate, another fantastic cooler, no fitment issues except 1. The front fan is a full 25mm deep fan, and my ram is 52mm tall, so the ram is in the way and I can't raise the fan high enough to clear. No problem, used a 120mm fan instead, fits perfectly, looks like. Cryorig hybrid version of the old NH-D14.
Years ago, gpus didn't have huge supporting backplates, so Noctua had no idea that was coming when they designed the NH-D15 and left mm of clearance from cooler and gpu. Then came backplates and suddenly the NH-D15 didn't fit, too wide. So Noctua bent the heatpipes and offset the cooler, fixed that, but there's also the popularity of RGB ram, and ppl didn't like the cpu cooler covering their expensive lighted ram. So ditch the front fan too. Slight performance loss, but not much. So the NH-D15S was developed.
None of which has any impact on your case choice 😉