This is a very good question, one I would have asked if I was buying now instead of a year ago.
Considering that great price for the S, the performance upgrades are not worth it, so you would be right on that. In this specific case, what WOULD make it worth it for me are the lights (+ KESSY). Unless you can retrofit the OEM adaptive headlights easily, your options would be aftermarket reps or leaving them as is (which sucks). Having dealt with aftermarket lights on my previous car, I would NOT consider it an option. No thank you, they almost always are a massive headache that isn't worth the hassle and/or a significant downgrade from the better OEM option.
In your case, I would suggest looking a bit harder. Seems strange you can't find ANY manual Sports? Wouldn't hurt to look out of state too. I picked mine up brand new when they just came out for $25K flat without any VW incentives (did not qualify) so now that the 2018s are ready to come in, I'm sure you can do better. Even if you grab one for $24K, the $3-4K premium would still be worth it to me for the headache saved in retrofitting an LSD, bigger brakes, and living without the LP. Oh, and the keyless system is great, really enjoy it.
If you can't find a good deal on a sport, I would just wait for the 2018s instead of settling on an S. May have to wait a few months for the dealers to realize they're not anything special and give big discounts on them. For me personally, the S makes sense for someone who would have otherwise just bought a golf but got a killer deal or someone who will strip the thing apart anyway to build a track beast. No point paying for parts you're gonna throw away.