See my comments in the report. Your patch makes the usabilily worse and counter-intuitive. I know, designing an intuitive user interface is difficult but we must try.
I think you want to say: "Let forget any usage of TPopupMenu inside the IDE Options / Project Option, because they are hidden somehow".
If so, I am agree.
The alternative of TPopupMenu is already, there:
1. TreeView. Eclipse IDE uses it in many "preference"
2. ListBox + Switch Button. Lazarus uses in Project Option: Form:
AutoCreateForm <-->AvailableForm
3 TextBox / Combobox. in Project Option Resources: Resource | Resource Type
All of above will be used together with current Matrix-Grid.
Is it you mean with "intuitive" ?