Hi, I think they were better together after about 6 weeks when they started using each other's preferred litter tray when it wasn't occupied. Before that, there was a lot of sitting outside the litter tray eating the hay. One or the other would also lie in the tray a lot, and they seemed to respect their claimed tray.
It was my boy who started jumping in with my girl, and she allowed him to share the tray with her. She is extremely placid, but bigger than him as she's a lionhead and he's a Netherland Dwarf.
8-9 weeks on and they have started swapping trays. My boy is less generous about letting my girl share if he's in it first. They are free range house rabbit with an uncaged base which was my boy's original territory before I adopted his little friend.
I think it also down to temperament. It took 6 months for my boy to bond with me, but once he did it was a strong bond. He is quite a feisty but skittish bunny. Unfortunately, he hates my husband and will lunge at him. So, if he didn't like someone, it would be obvious. My girl is very laid back and super sweet.
I read somewhere that once bunnies are home from bonding in a neutral place, it is the female who will most likely rise to the top. Therefore, I'm assuming that she is just sitting it out until my boy gives in. It's so funny to watch because she is so calm when he gets annoyed with her and will just ignore him when he wants to be groomed and doesn't seem to care if he nips her so stops pretty quickly.
It sounds like your bunnies are in the same situation as mine. They are bonded, but working out who is the actual boss. It will be interesting to see which ones become top bunnies.