Hmm.  

I would say this is him being territorial in the cage, because he views it as his space. Since they aren’t fully bonded, this could be why. 

Was this his cage before you started bonding them? This could be why he feels territorial in there. After he grunts/honks and chases her, he could feel like she understands this is his space and she is not welcome. Then when he feels she isn’t a threat anymore, he stops.

He could also be doing this at bedtime and waking-up-time because its when he has the most energy, like you said. He wouldn’t be displaying these action’s in the playpen because its their collective territory. 

You could try neutralizing the cage, which could stop his territorial behavior. Take the cage outside or in another room, spray down with a vinegar and water solution. Let it sit for a few minutes, then rinse very well with water. Dry it, and then repeat for the litter box if they use one. 

This will get rid of scents and make the cage neutral territory to both bunnies.  Let us know if these tips have helped, or if the behaviors continue! If he starts doing anything else, please note as well! 

Why are you putting them in the same cage when they’re not bonded? 

Thats true, didnt even think about that point!