Issues outlined here:
http://ez.no/developer/forum/suggestions/ini_priority_vs_extension_settings

New patch is online at github (12th july 2010):
branch: http://github.com/andrerom/ezpublish/tree/ini_loading_order
1st commit: http://github.com/andrerom/ezpublish/commit/9ecadd8ea7be7ff5bb75c4983dfffc43c82045f6

Patch changes ini loading order to become:
settings > extensions > extension-siteaccess > siteaccess > override
From:
settings > extension-siteaccess > siteaccess > extensions > override

This change solves long running issue in eZ Publish of not being able to override extension settings in siteaccess, which has resulted in half baked features like ActiveAccessExtensions and extension-siteacces and furthermore lots of enhancement requests to fix it by adding additional override levels.
So instead of making it even more complicated, this approach does a bc break that as of this writing does not cause any issues in default eZ Publish and it's extensions (issue in ezflow noted in comment bellow has been fixed in ezflow trunk).

Old text related to attached patch:

Technically:

• added support for extension/<myextension>/settings/override settings
• added support for extension/<myextension>/settings/siteaccess-override settings as proposed by Felix
• Introduces 'slots' on override dirs ( 'extension', 'extension-siteaccess', 'siteaccess', 'extension-siteaccess-override', 'extension-override', 'override' ) so they are kept separate internally.
• changed global override dirs to use protected static member instead of global variable
• cleaned up use of $identifier so it works as expected
• added support for 'multi pass' extension loading as described in forum thread
• added extension dir cache to improve performance ( modules, handlers and settings folders in extensions )
• and last but not least cleans up the ini loading order so it's like this:

  settings
  extension
  extension-siteaccess
  siteaccess
  extension-siteaccess-override
  extension-override
  override 
  

Related:
http://issues.ez.no/IssueView.php?Id=8049&activeItem=66