"It is better to change the file permissions with chmod() after creating the file."
The usual lacking of security knowledge within the PHP team rears its head once again. You *always* want to have the file created with the proper permission. Let me illustrate why:
(a) you create new file with read permissions
(b) an attacking script opens the file
(c) you chmod the file to remove read permissions
(d) you write sensitive data to the file
Now, you might think that the changes of an attacking script getting to open the file before you chmod them are low. And you're right. But low changes are never low enough - you want zero chance.
When creating a file that needs increased permissions, you always need to create the file with the proper permissions, and also create it with O_EXCL set. If you don't do an exclusive create, you end up with this scenario:
(a) attacker creates the file, makes it writable to everyone
(b) you open the file with restricted permissions, but since it already exists, the file is merely opened and the permissions left alone
(c) you write sensitive data into the insecure file
Detecting the latter scenario is possible, but it requires a bit of work. You have to check that the file's owner and group match the script's (that is, posix_geteuid(), not myuid()) and check the permissions - if any of those are incorrect, then the file is insecure - you can attempt to unlink() it and try again while logging a warning, of course.
The only time when it is reasonable or safe to chmod() a file after creating it is when you want to grant extra permissions instead of removing them. For example, it is completely safe to set the umask to 0077 and then chmoding the files you create afterward.
Doing truly secure programming in PHP is difficult as is, and advice like this in the documentation just makes things worse. Remember, kids, anything that applies to security in the C or UNIX worlds is 100% applicable to PHP. The best thing you can possibly do for yourself as a PHP programmer is to learn and understand secure C and UNIX programming techniques.