TBH, looks dirty to me.

For #41446 we can do similar to if (file_exists(dirname(__DIR__) . '/defines.php')):

if (file_exists(__DIR__ . '/defines-public-folder.php')) {
    include_once __DIR__ . '/defines-public-folder.php';
}

And you only check for

defined('JPATH_ROOT') || define('JPATH_ROOT', implode(DIRECTORY_SEPARATOR, $parts));
defined('JPATH_SITE') || define('JPATH_SITE', JPATH_ROOT);
defined('JPATH_PUBLIC') || define('JPATH_PUBLIC', JPATH_ROOT);

Then CLI script should generate only defines-public-folder.php not index.php

app.php then will be like:

...
if (file_exists(dirname(__DIR__) . '/defines.php')) {
    include_once dirname(__DIR__) . '/defines.php';
}
if (file_exists(__DIR__ . '/defines-public-folder.php')) {
    include_once __DIR__ . '/defines-public-folder.php';
}

if (!defined('_JDEFINES')) {
    define('JPATH_BASE', dirname(__DIR__));
    require_once JPATH_BASE . '/includes/defines.php';
}
...

Or we better call it defines-generated.php or defines-custom.php

I never understood way I only can override one variable or all in defines...
Because this means we broke all sites that uses it own defines file when we added the JPATH_API constant.

That's the reason I simple allow to override any constant for simplicity.

Then CLI script should generate only defines-public-folder.php not index.php

That was my initial approach to have only a custom defines (well I actually did a bit more) but I also like this take. It's simpler IMHO

Well, I wrote what I not like ?

At least please avoid hacking of index.php. create a separated file for generated defines.

I'm ok with either approaches, just make up your mind and let me know what will it be ?

I'm merging this for beta1 so we see any site effects and as it is needed as preparation for #41446