Just a question-do they have to be bonded or would you be able to live with them separately housed -but maybe able to see each other for company or play time (if that worked)?

Can you keep them together in a small-ish pen/area for a few days? If they’re fighting whenever they’re given more space, you might need to limit their space and *slooooowly* increase it over the course of days or weeks.

If it makes you feel any better, my buns did something similar during their bonding- Liam would demand grooms from Merida, and nip her when she didn’t do anything. This made her terrified of him during the bonding sessions, but they are now happily bonded (though they continue to hump each other haha- but no fights, so whatever floats their boat I guess). I kept them in a single x-pen for 2 weeks until I trusted them enough/had time to upgrade them to a larger enclosure.

I was thinking the same. Perhaps try them in a smaller area, even block of sides of the pen for real enclosed feel.

Are there any other pets or any other outside “stressors” you can think of that might set Matrix off?
Another thing that can trigger tiffs is when one becomes possesive about an item in their habitat. Like a hidey box or litterbox. Or food.

We’re trying to train Matrix not to nip at Dot so much (when we first got him, he’d nip at us really hard, but we’ve trained him out of that by saying, “Ow! No bite!”) but I’m not sure if the nipping is just old behavior from outdoor-hutch-bunny-life or if it’s a dominance thing.

That’s great you’ve trained him somewhat out of this behaviour! With yourselves, it’s easier to control your reaction to a nip. It’s harder to control Dots reaction. Do you use the same reprimand “no bite” when you see him nip her? She may grow more confident and stand her ground and hopefully he’ll overcome whatever triggers him.
It sounds like the trust level between them just needs to grow a bit more and that should come in time.

Aw, they’re really cute! I missed the link before.

Your lionhead has the old Dutch beard going on. :p Makes those cheeks look extra cute!