Firstly, PTW supports scenarios better than Civ3, so you wouldn't be overwriting files by playing the GOTM under PTW.
Secondly, conquests isn't (yet) being supported for three (main) reasons: 1.) Conquest still hasn't been patched to the final version. There are some significant changes being made to the game rules, and different people playing with different patches. This isn't a killer reason for not supporting conquests under the GOTM, but its still a significant reason!
2.) Conquests has such different rules to PTW and Civ3 that its not really practical to compare them side-by-side as we do with PTW v Civ3. Therefore, we would need to run it as a separate competition.
3.) Whilst we may do this in the future, we need to tidy-up the processes that we use for the current GOTMs: the results processing, QSC, Hall Of Fame and adapting our various utilities to support conquests. We will get there, but how we will support conquests and when we will support it will probably not be clear for six weeks or so.