Problems with websites meaning only unnecessarily expensive fares are shown? Surely not!
Seems to be a problem with how WebTIS separates out and return journey dates. National Rail Enquiries shows the fares correctly.
An Off Peak Day Travelcard is cheaper than the Anytime Day Return at £8.50 (vs £9.60) and valid any time from 0930 until 0429 the following day. I assume you want to buy online to benefit from some cashback scheme? If so just put in a return the same day, it will be just a valid.
Off-Peak fares are discounted by 12% on the Southern website. I have heard that there are also cashback schemes in operation.
To the OP: as for the safety of the last trains - pick one with a guard, and go to the front, as others have said. People who are bored or look tense will occasionally get bother - something like reading a book, eating/drinking something etc. will make you look slightly more relaxed, and you're less likely to get any attention. A thief generally won't primarily want to confront someone with a hot cup of coffee, or someone who has no valuables visible! I find late trains in this area are crowded and I've never had any real bother, even when severe delays have made some passengers frustrated. As for drunks, just move away, if you can, and don't make eye contact. Simple stuff, really!
The above said, I don't necessarily look like the sort of person you'd want to speak to late at night anyway! Maybe that's why I don't get any real bother.
And yes, I do have reason to use very late trains quite regularly enough to know what goes on.