Free-placed buildings work best when they have military value, IMO. It makes sense to build a stand-alone scout tower as a warning against invasions, or a military staging post where your troops can heal quickly after a battle...
Exactly the thinking behind our concept. We try to take away all the micromanagement from base building, evolving from BftME 1 interface, but at the same time free-building is essential for complex combat and economic experience. Again though we try to streamline the process, I`ll give you two examples.
Your peasants would always be able to build a fortified mining or lumber camp where it`s needed. And your soldiers will have the ability to build certain "structure" which we call Army Camp. Army Camps have multiple purpose, and can be user as either/and - healing, portable palisade fortress, siege weapons factory.