You are defining the $authen{user_module} variable three different times. Each time it is defined, it overwrites the previous setting, so the only thing that takes effect is the last definition, which in your case is in course.conf.
You should remove the $authen{user_module} block entirely from authen_LTI.conf and authen_LDAP.conf. If you are enabling multiple authentication methods, then the cleanest thing to do is set the list of authentication methods directly in localOverrides.conf.
Once you've done this, you can put the following after the two "include"s in localOverrides.conf:
$authen{user_module} = [
{ "*" => "WeBWorK::Authen::LTIAdvanced", }, #preferred authorization method
{ "*" => "WeBWorK::Authen::LDAP",}, #fallback authorization method 1
{ "*" => "WeBWorK::Authen::Basic_TheLastOption",} #fallback authorization method 2
];
This will enable both LTI and LDAP logins for all courses. If you only want this for a single course (or want to override it for a single course), then you can include it in course.conf, otherwise do not add anything to course.conf.