I agree Symlinks is not a good idea, but since the htaccess maker offers that option it would make sense to also offer the "safer" option (which doesn't have any security issues, and is usually enabled on hosts).
Regarding PHP. Php is typically run as "the user", which doesn't have any "global" permissions. However the Apache user needs to access static files such as images, but since it is typically not run as "the user", Apache needs to be added to "the user" group in order to access files in users home folder (and then "follow symlinks if user doesn't match" is really fun).
Again not a big deal, since nobody has rmentioned it yet.