It's really not that hard.
Imagine your car's suspension at whatever ride height.
What limits travel up?
Well upward, you want to top of the shock to contact the bumpstop and stop all further upward motion just before the tire hits the body or the control arms hit the frame. But on a Miata with stock suspension, the rear shocks would fully contact the bumpstops before you run out of travel upward. You could change that by installing a shock with a shorter body, but you have to remember that the travel of the suspension downward depends on the piston inside the shock not reaching the top of the shock, too.
So it's better to give a longer shock body more room to move upward by installing an extended top hat. The only thing there is that if you extend it too much, now the tire will hit the body or worse, the control arm will hit the frame. If you were only needing to add 1.5" of travel and you installed top hats that extend your upward travel by 2", then your bumpstops would need to be 0.5" longer.