Hi
Yes, but it falls out of the scheme that third party packages live in the same space as the distribution. If, for example, they were built to reside under /opt instead of replacing system files there would be a lot less chance of breakage.
There isnt really much stopping the repositories from making use of /opt for such purposes. If there are I havent heard of it yet. There are probably some issues over how path order is set to take use of whatever libraries that the packages are modifying that should take precedence for them.