Method 2 set permission on file system level, so not only for Apache. This is the secure way to set permission on a file.
Method 1 set permission on application layer but Method 2 also apply. If your content can't be read by Apache, then even if Method 1 tells that the client can read the file it will not be able to do it.
So the quick answer is No.
Method 2 will be used to ensure that Apache can read your php file but other users/process can't.
Method 1 will be used to protect page access with a password, etc...
I see you set the PHP tag, take care that Method 1 will never affect what a PHP could read or write. Method 2 as well as PHP configuration will do it.
/var is 755 root/root on my system, www will highly depend on your apache configuration and security you need.