reapply permissions post sql server restart
An alternative to modifying model might be to create a stored procedure in the master database that contains whatever you need to do. Then you mark this as startup proc (sp_procoption).
You might have to put in a WAITFOR in there in case SQL Server executes this before model has been recovered and tempdb has been created. For you to play with.
I've only used startup proc occasionally, so make sure you do thorough testing.
And, I fully agree with J.D.: modify them jobs instead, if at all possible.