Spare wheel kit was an option up to 2017 models. That had a space-saver, I believe you can fit a full size spare, but it raises the floor about an inch. As you say 2018 onwards have the sub-woofer on certain specs, don't know the implication of removing that, unfortunately.
I'm on my third CX since 2012 and have never needed a spare or to use the emergency inflation kit. Don't forget that Mazda assist covers roadside assistance anyway,
Alan