you buy a game, not a content thing, the emphasis on making the game and not on making it easiest and fun for the modding community, thats just an extra
alot of dm maps, specially the 1on1's were when they were made not ment for ut2004 retail but for another thing, and for this other thing it was ment for it would have been more appropriate to use mylevel
i dont know for ctf and as and the like, everyone just made what he liked and how he liked it, go with the flow
in the end its still -very- simple to find stuff in mylevel and to get it out
so its not such a big prob, it could only raise your filesize a little but that isnt such big issue either
if the game already takes 6 gig im sure those 5 meg extra in your map wont kill you