Free Build Mode, for those who've forgotten, allows you to build whatever you want, whether or not you have the materials, or perks, that you need. However, I've found vanilla items that I can't build in Free Build Mode. Free Build Mode set your resources, including caps, to 999. Now, I know of no settlement objects that require raw materials in anything like that quantity. However, all the tier 3 merchant stores, and some of the tier 2 stores, require 1000, or more, caps. As a result, in Free Build Mode, I can't create these, because I don't have the caps. But if I'm not in Free Build Mode, I don't have the perks. A somewhat Catch-22 flavour to this, now that I think about it.