There are quite a few potential reasons for a CTD when you change part of the campaign map; most likely would be a problem due to linked data from another file. For example, if you edit the map tga's to get rid of a region and replace it with sea, you need to make sure that the descr_strat file isn't trying to place things there which are inappropriate. When you introduce an entirely new region you need to make sure its name tag is present in the right places, and so on. Your best bet is to use the -show_err command line option all the time, and hopefully it will catch these errors for you.

The 21 faction limit only means that there can be a maximum of 21 factions present on any one campaign map. The descr_xxx.txt files in the /data directory allow you to modify almost all aspects of a faction's look, from the models and skins on the campaign map to the tech trees and what units are available and how they look on the battlefield. It's a very open system, which combined with the -mod command line option (which also redirects the campaign and battle directories) should allow you to create a wide range of nice things...

Hopefully that answers your question.