Not sure if I get you right. However, all configurations must be included in config_defaults_inc.php. The way a configuration option is evaluated is as follows:

1. Use database.
2. If not, then config_inc.php.
3. If not, then config_defaults_inc.php.

Within database, the priorities are as follows:
a. Options specific to user+project
b. Options specific to project / all users.
c. Options specific to user / all projects.
d. Options that apply to all users / all projects.

I think the order of b / c is correct, but I may be mistaken there.

Let me know if I'm missing something here.

There are several online configuration options available now under the administrator access level. Due to several items in config_defaults_inc.php which I have to study before deciding what I want to put in config_inc.php,
it would be good to re-organize within config_defaults_inc.php: two sections
Section one : those configurations that can be over-written via online configuration by administrator access level (i.e. manage **** functions, etc)
Section two : those configurations that can only be over-written via entries made in config_inc.php

For "Section two" there is an array $g_global_settings in config_defaults_inc.php

As mentioned by vboctor, all configs must exist in config_defaults_inc.php.

I also don't see any reason to change the structure of the file as suggested.