Interesting observation. I have several J-Nats and several Naguras, from soft to extremely hard.
I have a questione: did you flatten your nagura?
I always flatten one sinde slightly, so there are no high spots that can easily scratch a stone.
Even my hardest nagura do not scratch my stones unless I use them incorrectly: too much pressure, or unflattened.
Don´t jump into conclusion about the hardness of your stone and nagura because of random scratches from your nagura.
This doesn´t necessarily mean your Nagura is harder than your Ozuku.
However one thing kinda startles me, why did you asked for a Tomo Nagura softer than your Ozuku?
Usually you specifically ask for the hardest Tomonagura. I don´t see a problem because it probably doesn´t matter that much, but I´m curious