In the topic linked by @ben.turner, another point is made to move some constant from the local-bootstrap.php to the WP-Config and is implied that would solve the issue of xDebug halting on local-bootstrap.php. Since that topic is closed; this does not solve the issue.
The suggestion to set auto_prepend_file to none (not empty, but the actual value none) will prevent the local-bootstrap.php file to be loaded and that does solve the xDebug issue.
I’d like to go a step further and strongly suggest to remove the local-bootstrap.php completely. It is only used for auto-login, which can also be achieved by placing an MU-Plugin when the feature is used. No need to auto-prepend anything.