I have to agree with Kiwi on this one. Most of my mods are designed with the assumption that you're going to start the game with them.
They're built in such a way that if you add mods, or change settings, for the most part they'll change the game state so that things don't crash, but recipes will change.
though keep in mind that when I wrote most of these mods, pretty much every time the game received more than a bug-fix patch, a Recipe somewhere was changed. Some of the major ones even deleted or changed the size of buildings, requiring you to make changes to your base.
In a climate like this, requiring you to make modifications to your production chains felt like something minor.
Also keep in mind that while my mods did mostly just add things in the beginning, most people were requesting more "Integration" with Vanilla. This means changing recipes to use my materials instead of vanilla materials, like Aluminium and Titanium for the low density structure, instead of steel.