I think what the article means is that you cannot install for example SSIS 2012 twice on the same machine, but you can install SSIS 2008 and 2012 on the same machine. You'd have to modify one of the configuration files of the service though, to point to the correct MSDB database.

The problem is that SSIS is instance unaware, so SSMS will look for only one instance. Not sure on how to solve this.