No particular reason, I have just never seen it done before. The only possible down side would be zipper damage.
That could be an issue, but I don't worry about it too much. At least so far it has not been an issue. Maybe if one of the zipper pulls happened to get in a wrong position it might damage the fabric. However, I had a tent that had rings with about an inch and a half long pin on all 4 corners. I was really concerned about these and made sure they were all at the top of the bag (even hanging out side the bag between the bag and the compression flap), and hopefully not puncturing any fabric.
The tent does not necessarily have to go into a waterproof bag. It just happens that sil-nylon is pretty waterproof, and makes a nice, light compression sack. I believe that being waterproof is just a bonus. It keeps a wet tent from getting other things wet. A rolled up wet tent and rainfly are not going to dry on the back of the bike. There are too many coated surfaces to let water out. Sometimes when my tent is relatively dry, but my rainfly is wet, either through rain or condensation or both, I'll put it and the sil-nylon ground cloth in a plastic grocery bag and put the tent in the compression sack. All the items go in my rackpack with my sleeping bag and pad. I've not had a problem with my sleeping bag getting wet. We had 35 days of rain on a 3-month tour in 2011. In that situation it was a challenge keeping things from getting damp.
Sometimes we just got a motel room and dried things out. It was still raining
