I booked my flights from PRG to JNB via FCO well in advance and immediately went for the Plusgrade offer.
They required 50 EUR for short-haul segment PRG - FCO - I offered 60 and never got an upgrade.
For FCO - JNB they required around 420 EUR, I offered 480 and got my upgrade from economy to business exactly 48 hours before departure, at the time when check-in opened. I was able to select the seat and I am looking for enjoying the flight.
Just reminder - as you upgrade the long-haul leg, also the short-haul segment has Skypriority tag, so you will be able to enjoy fast track and priority boarding so I think there is no need for the upgrade on short-haul segments.
Safe travels!