Gearbox fine, put it through basic settings a couple of weeks back. Although if cold and I sit in drive with my foot on the brake it makes a quiet noise which goes if I click it in neutral. Think that's normal though.
Assume this is with it in drive with brakes on? - yes normal, that's the clutch slipping.
I am not really hearing any particular stand out noises in your video - BTW it worked for me in Google before the youtube version.
Subframe creaking / knocking is a common issue on Mk5's where subframe bolts stretch, only reported occuring when pulling away.