I think the big issue is asset control and implementing a system that allows fan creations without displacing a market for the original content. Most developers have the same policy regardless of what publishers want and that is: design a system where fans do not compete with the developers themselves. This usually translates into mods that extend the game in diverse ways such as implementing unrelated games like CTF, DM, TD, hero battles, etc. I have not encountered a major production that allows mods and total conversions in similar style to expansion type content. In order words, your creations cannot be based on or extend cannon. However, dev time to create the proper tools and moderate an eco system conducive of mods can be resource intensive. The earliest games with total conversion type mods were shooter; the assets were mostly art and impinging on existing IP was minimal.
Naturally every situation is different and each developer has its reasons for allowing or disallowing mods; and policy on what type of mods are permitted, if any.
