The main considerations on that front are patching and Content Manager related.
On the patching side, it is important to check which folder it is attempting to patch before you start the process.
On the Content Manager side, it will default to the last used version of Content Manager for it's file associations, but my Trainz Protocol Changer can override it.
In terms of messing up previous installs, this is unlikely apart from what is mentioned above, although to be safe it's best to install all the versions as standalone versions and not as an addon pack if prompted.
Shane