In 2008 when YOURLS consisted of a dozen files I thought it would be smart and frugal not to always load everything, in particular functions-install.php and functions-upgrade.php that are rarely used.

This is over optimization. Simplify the start logic and just always require() them (includes/Config/*, admin/install.php, admin/upgrade.php, tests/bootstrap.php, tests/tests/install/install.php)