Sorry, I thought the Nebari referred to the very low knuckle part of the trunk
It refers to a flare of surface roots. At this stage you cannot talk about Nebari yet.
So, should I not even prune back every second new leaf?
Nope. It's too young and too small to be pruned at this stage.
What about fertilising?
Yes please. Follow the instructions on your fertilizer product.
And the pebbles are just for show. Would that cause the pot to contain TOO much moisture and in turn cause root rot?
It will prevent you from properly seeing when the plant needs water. On bonsai, it's not done, as it doesn't look good.
Only cheap wholesale 'bonsai' have pebbles.