The base flashing is not on top of the shingles. It is installed as it should be. The bottom part does go over the shingles at the bottom. Some get fancy and muck a tab over the flange at the bottom, but that only creates a damn for the water coming down the sides to back up against. The silicone all over everything is not needed if done properly. The only place there should be silicone is around whee the pipe meets the base flashing and around the storm collar.
The OP's is installed correctly. doug crane's post was a response to my observation in the post before his.