Hi Peter,
Pretty common question.
Company_phone file is used to normalise the address book that is download to the client and normalizes the phone numbers that are taken from AD. Here is a good blog that talks about this aspect
http://blogs.pointbridge.com/Blogs/schertz_jeff/Pages/Post.aspx?_ID=17.
Location profile normalization rules normalizes number input manually at the client, this is either the default for the pool or in R2 you can set this per user.
The location profile and normalization rules set at the medation server is for inbound calls.
Hope this helps. Your right, this can be confusing to someone new to OCS.
Cheers
Chris
http://voipnorm.blogspot.com/