I’ve done it with other (similar) tents, but only in really good weather. It would be pretty easy for rain or dust to get in there. You suggested putting rocks on it, which is a good idea. That would prevent it from flapping around and getting dirty. But if I thought there was a decent chance of rain I would probably disassemble it, put it in a bag (with the fly on the outside) and then turn the bag over and set it on a surface that can drain. Same with the sleeping bag and pad. You could also just carry a big bag and put all the stuff in it, twist it up nice and neat, then hang it. Of course the big drawback is setting up the tent every day (you lose one of the nice things about base camping).
Another alternative is to just get one tent pole and use it. I bought a pair years ago for a TarpTent Squall 2 (when I didn’t carry poles). They only weigh two ounces a piece. Now I just carry one if I’m doing a lot of base camping. I can set up my Refuge X using one pole. It looks weird, and I wouldn’t want to sleep with it like that, but it is off the ground, and would handle a rain just fine (keeping everything inside dry). When I get back to camp, I don’t need to re-stake, but just adjust the lines a bit and put back the poles (I sometimes just leave the tent pole on one side with the trekking pole on the other).