Is there any real game/save breaking danger to worry about when using console commands to place various building pieces (walls mostly but also floors) into precise locations (often clipping through/into stuff)?

I'm customizing/refinishing Home Plate into a nice wood paneled/crafted den/cabin looking interior. I'm covering up ALL the nasty rusted metal on the ceiling and basically covering all surfaces with wall and floor pieces from the Alternate settlement mod. Without console positioning (modpos x,y,z) in most places you can't even get CLOSE to close enough. I'm using the light grey colored floors as CEILING and floors.

Nope, manipulate to your hearts desire! Theres a mod that does it easier and better.. http://www.nexusmods.com/fallout4/mods/9424/? (Requires SKSE).