[FEATURE] Allow directory structure override

This patch introduces a new setting in TYPO3_CONF_VARS that allows
overriding the default directory structure:

$GLOBALS['TYPO3_CONF_VARS']['INSTALL']['overrideDefaultStructure']

The configuration array is transformed from an indexed array to
an associative array to make overriding possible by using
ArrayUtility::mergeRecursiveWithOverrule().

Resolves: #61642
Releases: 6.3