I think I can see what is happening:

1. Based on your screenshot it appears that in the project area Jazz Test the Architect role has been granted permission for all source control operations. In the team area the Architect role has been denied permission to perform any of those operations. The team area permissions are not so easy to read because there are actually three states that a permission can have: permitted, denied or inherited from the parent. In this case the parent is the project area Jazz Test. In the web client if a permission is inherited it's label will be in regular type, if it permitted or denied the label will be in bold type. I can see that in the screenshot of team area RTC the labels for all of the source control operations are bold, meaning that those permissions will be denied, overriding the settings from the project area JazzTest,

I think that the best way to allow the Architect role in the RTC team to perform the same tasks as an Architect could in Jazz Test is to clear the override for each of the operations under Source Control. To do this open the RTC team area in the Web Client (  or Eclipse Client if you prefer ) and select each of the source control operations Deliver, Replicate Change Sets etc in turn and click on the clear override button.

2. Final can only be applied to elements at the second level of the tree, that is the level of Deliver, Replicate change sets etc. At all other levels the final checkbox is grayed out.

3. There is unfortunately no quick way to set all the permissions for an iteration to unconfigured.

There are a couple of articles of which explain more about how permissions work: https://jazz.net/library/article/291 and https://jazz.net/library/article/292. We are also working on redesigning the permissions UI to make it easier to use - you are far from being the first person who has found the permissions UI hard to use. See https://jazz.net/jazz/web/projects/Jazz%20Foundation#action=com.ibm.team.workitem.viewWorkItem&id=246821 .