The SQL Agent has always been seperate fro the actualy SQL Server (at least back to SQL 6.5, but probably further).
The reason to run the agent as a different account is to lower the permissions that the SQL Agent would run under when it's connecting to the SQL Server. The Windows account that SQL Server runs under is a sysadmin within the SQL Server. The SQL Agent is typically also a sysadmin, however it does not need to be. Some people like to limit the rights that the agent has so that the agent can not go out of control.
Personally I typically have them run under the same windows account.
Denny
MCSA (2003) / MCDBA (SQL 2000)
MCTS (SQL 2005 / Microsoft Windows SharePoint Services 3.0: Configuration / Microsoft Office SharePoint Server 2007: Configuration)
MCITP Database Administrator (SQL 2005) / Database Developer (SQL 2005)
--Anything is possible. All it takes is a little research. (Me)
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