I like to keep my overrides in the override directory, as I think it's more logic to seperate them from the pagelayout file with includes.
Also, if you have the need of overriding ezxmltags or something, they are to be placed in the override directory with the same directory structure as in the standard folder. Those won't have to be specified in your override.ini.append.
Well, that's my point of view - Now for some coffee.
If you are trying to override a template that currently exists you must put *your* new template into the overrides directory. Thats where ez will expect your override to be.
When you declare an override, as you given in your example, it must be put into the templates/override directory otherwise ez falls back on the original.
No, its like intented. After experimenting (and the course in Skien), this the current status: there are actually 3 levels / places which determine which templates are used.
The default is to use: /design/standard/templates/.....
This can be overriden by templates in exactly the same directory structure inside /design/<yourdesign>/templates. You can call this the "default" site specific templates. (you may copy the entire folder inside /design/standard/templates/ to this one if you want to make changes to the defaults from standard).
The third one (and which has precedence over the above two) is through the override.ini file. What you specify here lives in /design/<yourdesign>/override/templates if you specify a SubDir=templates
