I've yet to drive the 981 Cayman, but I've driven the same Boxster plenty in both guises and with manual and PDK 'box. For me, there's no right or wrong answer.
They're both very wringable engines, so using all the revs isn't a chore. You'll have less opportunities to do that in the S unless you don't care about your licence, if that's a consideration at all. The S has a better spec as standard and the biggest one that cannot be (cheaply) fixed is the brakes: The red calipers signify the bigger and better brakes on the S. During normal road driving I found little to choose between them, but if you were seriously working them (Alpine switchbacks as well as the obvious trackwork) then you'd want the bigger ones.
The optional PASM includes a 10mm drop which makes a massive difference visually, especially if you're going for anything other than the 20" wheels. FWIW I would also choose the 19" Boxster S wheels, best out of a bad bunch by far. The PASM is no longer seen as a must-have with the larger wheels either, even on the bigger wheels the ride is fine. That said, you may wish to wait a couple of months until the Sport Chassis option is on the configurator, as this will give you a firmer springs, dampers and ARBs with a 20mm drop, and it's only £688. I'd consider that a must-have if it were me, especially if you're not going for PASM.
If you're having a PDK car, then Sport Chrono is an absolute must-have. No two ways about it, it transforms the PDK 'box and you will want this! Try the regular stereo before getting the Bose, it's more than adequate and you can put that money elsewhere.
Everything is very much down to personal choice. Personally I would choose a well-specced non-S car over a poverty spec S, but neither would be a bad choice. Who is your local OPC? Give them a call and speak to them to sort your test drive out, don't rely on the configurator to send stuff over to them. I know my local one is running both a manual non-S and a PDK S Cayman as demo cars, so you could (and should) try both before committing.