Disk Utility will not repair permissions
Using answer space for formatting &amp; 'comment size', I'm not sure this is really a full 'fix', but perhaps a pointer in the right direction. It can be updated/amended to get to the correct answer, if needs be.

Note: Permissions on symbolic links have no effect. You need to check the permissions on the target file/directory - though in fact the perms are 'correct' in this case, it's the links themselves that are not as expected.

Permissions differ on "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html"; should be lrwxr-xr-x ; they are -rwxr-xr-x
means that the Finder thinks that file ought to be a symbolic link, but it isn't - the link has been broken somehow.

On my machine, that link is to /Library/Documentation/Resources/Eagle/index.html

Fix == remake that link
From  OSX Daily:How to Create Symbolic Links at Command Line of Mac OS X  


  How to Make a Symbolic Link
  The basic syntax for creating a symbolic link (or soft link) is as follows:
  
  ln -s /path/to/original/ /path/to/link
  
  That will point /path/to/link to the original location, in this case
  /path/to/original/


Permissions differ on "Applications/Safari.app/Contents/MacOS/SafariForWebKitDevelopment"; should be -rwxr-xr-x ; they are lrwxr-xr-x
thinks that one should just be a file... but it's a link.

Mine is a link too, on El Capitan - [which I'm assuming you're not on, as you still have a 'Fix Permissions' option in Disk Utility] - to 
/Library/Application Support/Apple/Safari/SafariForWebKitDevelopment  

I'm tempted to say in that case, leave it as is.
Checking perms on El Capitan from terminal gives no error on that one.

Edit:
I missed the first one -
Permissions differ on "tmp"; should be drwxrwxrwt ; they are lrwxrwxrwt

Mine is a link too - to /private/tmp so I'd leave that one alone too.