Official comment
You can - provided you match the pitch position.
Let's say deck 1 is a track at 128BPM and deck 2 is a track at 120BPM. Both hardware pitch faders are at 0%, but you're playing deck 1 and use the SYNC to match deck 2.
Deck 2 now has a software pitch of 6.67% (rounded), but the hardware is at the 0% position. Once it becomes the master deck you can't adjust the pitch until you've moved the hardware fader to match the software fader position. This is known as a "software pick-up."
In Serato's operation, you can move the fader at any time and the fader position and movement is relative, but in rekordbox, the fader is absolute, and you must move the hardware to match the software first.
You will get the hang of it eventually. ;)