Yes, your stem is flipped down.

2cm is well within normal tolerances for saddle height due to differences in pedals, shoes, clips (if applicable), shorts, and toe angle. If the saddle is too high you'll feel your hips rocking side to side or your feet will feel toe-down. Keep in mind that moving the saddle up also moves it back, you should move it forward ~6mm if you raise it 2cm to keep your saddle to handlebar reach the same.

Once you get on some longer rides, you'll get a better idea of what works and what doesn't.