-it will add new armor and don't touch vanilla (including esp/esm mods)
-or it will replace meshes/textures for existing armors without esp/esm
Alternative start don't change anything about main quest line, so you will be able to continuw your journey.
titan357 is right, you simply have hole in your history.
But keep in mind- some beginnings (f.e. raiders, talons) can make your main quest progress impossible or more difficult due to faction's relations. So- don't mess with the Brozerhood of Steel And with Rivet City security.
Thanks for the info. Now to reinstall Exnems Female Body Replacer Mod which changes the look of female vanilla armors with meshes and textures with no esm and esp.
I chose Vault Dweller for Alternative Start to fully enjoy the harshness of FWE. Regulator and Mechanic are cool especially with the new weapons one starts out with but i wasnt ready for that kind of firepower from the get go for my latest character.