Not much from what I understand. It's just that apps like Google Play and stuff will see your phone as running Marky Beats instead of CTMod. It will allow you to download apps that G Play normally wouldn't allow you to download with CTMod.
Just make absolutely sure that you make a CWM backup before you try it.
I'm sure that Blood or one of the other guys could break it down better for you but as for ill effects, I don't think their will be any. Guys do it over in the TF300T section of XDA every now and then.
EDIT:
If you're doing it so you can get an app from G play, you can change the build.prop back after you have downloaded and installed the app.