Good thread about the internals of the Nexus 7 here. Interesting that it has 2 disabled/unused gears one of which is the direct drive gear 1:1 but it shows the 2 low gears are partially direct gears as are the 2 highest with the middle gears in-between utilising both the increased and reduced gearing.
https://forum.cyclinguk.org/viewtopic.php?f=5&t=80888
On the Nexus instruction sheet which is identical for both 3000 and 3001 it says you should expect noise while operating in all but gear #1. Which makes sense looking at that forum posting.
I've got a Nexus 8 on my Carrera Subway 8 and could never use the direct drive gear, it just was never the gear I wanted to use apart from rare occasions. My cycling style seems to be I need 3 gears for hill climbing and 1 gear for flats and downhill. On the Nexus 8 I'm using gears 1-3 and then 8 with the in-between gears used only fleetingly. So in a way the Nexus 7 is setup better for me as overall the gears with extra complexity and less efficiency are the middle gears I wouldn't use.