The thing is, your techniques will affect a pretty good number of maps. Anyway, you're going to have to take into consideration that a good number of mappers (maybe all of them) won't want to dirty up their map names with the ctp.
Too be perfectly frank, in this game it won't be up to the mappers either way. If there's admins who don't want the ctp1_ muck, they'll take it off, and there's good admins who'll add it to maps that need the prefix. Too be honest, the ctp1_ prefix is a safety next, but in reality if the name is changed, then people will see that ctp1/lol.jpg is missing..
A person could use a suffix too, it doesn't matter. I AM trying to standardize it NOW so that we don't have to worry about this later.
Just to let everyone know before more criticism comes my way...
The plan for 1.0 is to use an installer so all the installation problem will be fixed. And 2.0 will include an installer that will check for /ctp1/ and if it's not found, it will copy it. I wonder if there's a way with NSIS to check to see if the files have been modified and to change them back if they have...
For 2.0, think of it as 'a stand-alone expansion-pack' in a sense.