Sorry , was in a bit of a hurry and couldn't find the right words . Any layout related changes shouldn't be injected in any 'default' magento layout files , like you specified previously (i.e. catalog.xml , customer.xml and local.xml being one of them as well).

1. Because theme fallback mechanism will ensure that the layout files from the current theme will be merged , along with those that have been injected via layout update , but are not found under the current theme 'layout' folder.
2. Nodes under 'local.xml' will be merged at the end of the process (for which the Config Model is responsible) , meaning that they are 'final' (similar to final keyword in PHP).

For illustration :
theme A (default)
theme B (mytheme) - both under the same package , theme B being the current theme used

Both themes have a local.xml defined , but the nodes from theme A are not merged (which could be a good thing , or not) . Worse case is when you have a module with a layout update which needs specific layout changes that are found under local.xml . This means committing a revision under this module scope that changes local.xml , which in my view is not ideal (all layout related logic should be encapsulated under the module's layout file which has been injected via layout update in config.xml).

Let me know what you think.