Removing "Delete" option from the Portfolio level ensures the Portfolio Manager can't “Delete” the Portfolio itself but that doesn't mean he/she won't be able to “Delete” Projects under the Portfolio.
Portfolio Owners can “Delete” Projects even if the “Delete” option is not enabled at Portfolio level
- The Permissions they get on the Projects are inherited from the Portfolio. Removing “Delete” option on the Portfolio won't let them “Delete” the Portfolio itself, but won't affect their ability to “Delete” Projects under that Portfolio.
- The mentioned settings on the Template will take effect if you, for example, create a Project from that Template, don't change anything in the Access settings and give any User (with a plan license of course) Manage access to the Project itself. In this case they will get Manage without “Delete” access as defined.
- In any case the User gets the highest Access given to the object. So, if from the Project Settings you remove “Delete” option for “Manage” Access users, but the user has Manage access coming from the Portfolio (with or without “Delete” option checked on the Portfolio level) he will be able to “Delete” Projects under that Portfolio.
If you still would like those Users not to be able to “Delete” Projects at all, please go to their Access Levels (Setup -> Access Levels) Edit them and remove the ability to "Delete" Projects.