Some do it because the extra weight of a bigger tire and aftermarket wheel is too much for the tailgate to support with out expensive mods. Or on a steep incline when off-roading you can catch the spare and destroy your tailgate. Some just do it for looks.
Both of the above is why I did it (minus just for looks) but also moving it into the jeep distributes that weight of the wheel and tire (120+lbs) over the rear axle instead of at the back of the vehicle and it makes it more balanced and stable for crawling technical trails (not as tippy and the front doesnt lift as much).
The drawback is you do end up losing storage space if you go with an interior mount like i did but I still have rear seating and plan on getting an offroad teardrop in the near future to resolve any travel storage issues.