In a word, no. If your Steam installation is in program files, windows User Account Control can get finicky if you try to change any of the files; so it might behoove you to move Fallout 4 (or Steam entirely) out of Program Files. But Steam itself won't get in the way.
If you're just looking to install mods, just find a mod manager like the Nexus Mod Manager (or look up the .ini edits) in order to get around the launcher disabling any plugins on startup. That, and read installation instructions for everything you install and keep backups of your existing saves.
If you're looking to make mods, the official Creation Kit will be coming out within the next few months (could be tomorrow, could be february); if you want to prepare for that, look at the Creation Kit wiki and some youtube tutorials for Skyrim. It'll have differences from the Fallout 4 version, but it'll get you off to a good start. There's also FO4Edit, which is a pretty handy tool made by the community, that you should look into - although it's still in early stages and they won't be able to figure out everything about Fallout 4's inner workings until the tools come out. Nifskope if you plan on making models/textures, and the Fallout 4 Script Extender if you're interested in the scripting/coding side - although again, everything's sort of in a weird state until the official Creation Kit comes out and the community can really sink it's teeth into the game.