The procedure changed either last year or the year before. Forms now have to be sent to Rail Staff Travel to be authorised. It should also be noted that Active staff can generally apply directly to RSTL, rather than going through their Employer, thereby cutting out the middle man.
You helped me out with a similar situation in another thread. Member of staff was not bothered about the form when he loaded my STC onto a (new) Oyster Card for the first time yesterday at Tottenham Hale. If they took the form in, it'll probably end up getting stuffed into their pocket or lost before the end of their shift. At least ticket offices could keep them and presumably send them somewhere with other paperwork.
One thing to bear in mind is I saw three options on the menu - TfL Rail, All Rail and All Rail-N. Not sure what the latter means, but my first attempt yesterday only TfL Rail was loaded on. After a journey from Tottenham Hale to Stratford (direct) earlier today, I ended up getting charged full price. However, a helpful member of staff at Stratford changed the reduction correctly to All Rail. Coming back the same way, it correctly discounted the fare.
Phil