Actually I got an official Mountain Lion image from Apple way back 10 years ago, and ever since a new MacOS was out, I just copied my latest VM and run that one as a complete update. Couple hours later I was having their latest OS in new VM. So all my VM's have official Apple software, no 3rd party included. And yes, you are right, every time a new update for apps I use appear on store, I get hit with the message to update what I have. I simply just cancel and go on with my work. XCode is the most updated, I get hit with messages for it at least several times per week.