You dont have to be confused. It is pretty simple.
When you login as a certain responsibility Oracle will try to look for the necessary profile options first at the responsibility level.
If nothing is found there then Oracle will look at the Application level. If nothing is found there then Oracle will look at the Site level. This is how it works.
Usually most commonly used profile options at specified at the Site level so that you dont have to override them at the responsibility level.
For example if 8 of out 10 of your responsibilities are pointing to ledger A and 2 to ledger B then one way to implement this would be the following:

Site -> GL:Data Access Set = Ledger A
GL Responsibility 9 -> GL:Data Access Set = Ledger B
GL Responsibility 10-> GL:Data Access Set = Ledger B

Outcome:
GL Responsibilities 1 to 8 will point to ledger A
and GL Responsibilities 9 to 10 will point to ledger B

There are always exceptions. Some profile options are mandatory to be specified at Site level and some at responsibility level and so on.
Some profile options are be overwritten at User level as well (e.g. Printer).