As far as I can gather from previous experience the layout master only likes 1 instance of a portal feature
That is only true for a few controls like <portal:ScriptLoader, <portal:StyleSheetCombiner, <asp:ScriptManager, there should only be one of each of those but most other controls such as <portal:WelcomeMessage can be used multiple times.
Probably the mistake you made that caused you to believe there can be only one is you copied and pasted it but didn't give the new copy a different id. IDs must be unique on server controls or it causes errors. So you can use more than one but they each must have different ids.
Those controls are not CMS plugins so they cannot be added to top pane without making a custom feature control and embedding them inside that, then add the custom feature to the page in the top pane. But they can be used anywhere in layout.master and they can be used multiple times in layout.master so long as they have unique ids.
Hope that helps,