I had removed the hard top last year. You can do it yourself if you have access to 1 or 2 of your friends who can help lift the hard top. All you need is the tool set provided by Jeep to remove it.
I had stored in my parking lot, Being the last car in the row I have some space besides my parking, alternatively you may use one of those standing lift storage systems or strollers in the designated parking space itself.
i use tool bags for storing all my gear they don’t move around and easier to move in and out of the car. I have 3 bags, 1 with 3 piece AOR shovel, kinetic rope, 2 with tools 3 with Air tools (air hose etc). I keep the first recovery bag in the passenger side foot rest, rest two behind the front seats between in rear seats, they don’t move or rattle as well. Alternatively you can put it in the rear and strap them for extra security.
Last year after I removed the top and drove in the sand, a lot of sand slid into the speakers and they stated to make rattling sound and had hard time getting rid of it. Had a heater button failure (tho it happened after I put back the roof) and finally when i had it fixed that the mechanics cleaned all the sand.
However exciting it seems, frankly it’s not worth the trouble to remove it for the desert. And as it is a Jeep already makes awful lot of noise and even more after you remove the top. Plus the dust and heat. While the temperature readings on the weather app shows lower temps the actual on road temps are too high. Removing tops in US makes sense where they don’t have all the dust like we have while going off-roading in the mountains & rock crawling etc.
I am more concerned about dust and sand in my car because my Jeep is a daily driver and I like a clean car. I go lengths to make sure that the car interiors are in perfect condition (tho if one were to look at anytime might differ that ascertion - since as a off-road car as well, you can do only so much)
Having said all that you - need to experience the fun of topless car first hand, you do. So go ahead remove it and put it in your parking spot. if you have a designated covered parking I am sure no one will flick it off that location.