Actually, the "Master Page" link is not always shown under Look and Feel column. It is appeared Only when you activate the "Office SharePoint Server Publishing Infrastructure" feature from Site Collection Features page. Otherwise, there will be show "Top link bar" link instead.
When you open the "Site Master Page Settings" page after you click the "Master Page" link under Look and Feel column. You can see two major parts in this page. The one is Site Master Page and the other one is System Master Page.
1. System Master Page:
This setting only effects the pages with masterpagefile="~masterurl/default.master" property. The page will be changed to use the master page which you specified in System Master Page portion instead of original default.master in runtime.
2. Site Master Page:
This setting only effects the pages with masterpagefile="~masterurl/custom.master" property. The page will be changed to use the master page which you specified in Site Master Page portino instead of original custom.master in runtime.
So, if you want to keep your all site contents have consistent style. You'd better to change Site Master Page and System Master Page setting at one time.
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