What is the right way to update a Prefab in a team environment?

Currently we're using Unity Pro 4.1.5 and our project is checked into Git. I'm new to Unity but as I understand it, to make changes to a Prefab you drag it from the Project into your Scene (to instantiate a working copy), make changes in the Inspector, apply those changes back to the prefab and then remove the instance from your scene.

However, in even the most basic instance - changing the position of an embedded GameObject and pressing the Inspector's Apply Prefab button - the resulting changes in the .prefab file are extensive and unexpected. The diff contains hundreds of changed lines on child objects that I did not modify - things like "serializedVersion" being incremented, "m_Enabled" flipping from 0 to 1, "m_Script" attributes changing their 'type' from 1 to 3 and more.

The "m_Enabled" change is the most troubling - if the Prefab was setup to have disabled parts by default, why are they being instantiated as enabled and why are those changes percolating back to the Prefab when I did not press Apply on any child object except the one I repositioned? When the game is played, the Prefab is broken because all child components are enabled by default.

I've had to manually go line-by-line through the diff and revert the unnecessary changes leaving only one change to "m_LocalPosition" attribute before I commit. When I do this, the game plays as expected and the element I repositioned appears in the correct spot.

I feel like I must be missing something obvious - what do I need to do to prevent Unity from generating hundreds of unnecessary changes to the .prefab file? What is the right way to manage this on a team when it appears so easy to inadvertently change objects? Thanks in advance.