Maybe this will be possible in future, but at the moment it's very complicated since mods aren't as easy to install as plugins. Mods are more likely to conflict with each other.
Andreas, I think you're right that the mods conflict with each other, but in case of conflict what could be done is to close the server. This is already implemented in most hosts and seems to me a very basic option
We want to keep our system as easy as possible for our users.
If we would just stop the server many users have to wait in the queue again and don't even know why their server stopped. Working with mods, especially if you are new to this topic, is very complicated.