Invoke hook_menu_link_alter after setting default link item structure

Currently some modules rely on not required parameters of a link item in their hook_menu_link_alter implementation.
This leads to unnecessary notices about undefined indexes etc.
One way to solve this would be to invoke the alter hook after the defaults are set. But in the worst case this could break some of the checks of contrib modules. The other way is to fix all the contrib modules.
Currently I'm not sure how to proceed here - suggestions?

I've attached a patch which invokes hook_menu_link_alter after the default definition.