No. These are two separate programs, and all the files for one version are completely independent from the other version. Installing them to the same directory will only make it difficult to remove either one individually.
Note: If you have Study Notes or verse additions to the Treasury, your older Version 2 files will be found when installing Version 3 and converted or saved in your new 3.0 directory. We recommend you make a backup copy of any important files, such as your Study Notes, before installing Version 3.