To your question:
The reason for that is web development technologies are changing. A theme or plugin company or even WordPress could change any time and the theme and plugins must adapt to that change. Another reason for changing or updating the system is for improvement and fix problems experienced in the past.
In web development or even in general programming, there would always be breaking changes especially during major updates as I’ve said above.
It’s not just X and Cornerstone update that could break your site. A major WordPress update could break things too.
That is why having frequent website backups and a test copy of your site is vital for website owners. It is a standard in web development to test updates in a staging copy of a website.
Now regarding the conflicting plugin, we don’t have support for plugin conflicts but it would be in our interest to know what plugins are conflicting with Cornerstone so we can improve it if possible.
Please tell us the name of the conflicting plugin and we’ll test it. Just note that because we don’t provide support for plugin and custom code conflicts, we can’t guarantee a fix.
You should report the issue to the 3rd party plugin author also why his plugin breaks Cornerstone.