In the extension finder is some code which removes the phpbb_root_path (but only if it is "./") and reappends it for the checks later.
When your front-end file is not inside the phpbb root, but a subfolder and therefor your root path is "../" it does not get removed, but is prepended later again. The the finder tries to locate the extensions in ../../ instead of ../
This function in phpBB\includes\extension\finder.php must be modified to replace the first occurance of
and afterwards remove all