Well, I have not seen extend.dat listed in the PUP section by default.
My guess is that someone made this a 'default' in your environment to force the deletion of this file.
Extend.dat had limited value for Outlook 2007 and before. If an add-on changed inside of Outlook, Extend.dat was suppose to 'cache' the loading of the add-on which was meant to speed up the Outlook launch. Unfortunately, sometimes the cached information didn't match actual add-ons, then Outlook would fail to launch properly. Deleting extend.dat was the solution.
No bad effects from deleting this file as when Outlook opens, it will simply reconstruct the file. Outlook 2010 (and presumably later) ignores this file.
This has nothing to do with which version of VSE you have. If you want continued to remove extend.dat, continue with the rule. Otherwise, simplify your PUP list and remove the rule.