Yes unless directed to another location for mod placement, for example the Font mod goes into a different area all together.
But what we've found out and I believe is the latest, for many mods you just keep adding them to an existing mod, so there are no restarts. In most cases that should work.
There is now a method to adding a mod to an existing games without mods, I haven't tried it personally.
There is also a Blank Base Mod, which if you are lucky and see and install that before you start a game. Even though it does nothing, it opens you to add mods at any point with relative ease.
