If I do an installation with the 2008 installer, the 2008r2+ installer happily overwrites files in the same directory and the system thinks I have both products installed but I really only have the files from the most recent one I installed.

We could:
1) Leave the behavior this way, which is confusing
2) Use separate install directories so they can co-exist peacefully
3) Complain on install of overwriting files
4) Include both sets of files in a single MSI and choose which ones to install automatically (and thus make it harder or impossible to run non-2008r2+ builds on machines capable of running them)
5) Include both sets of files in a single MSI and let the user choose which to install, defaulting to the most performant version the installation target will run