Whew.... you just reminded me in living color what living with multiple dogs was like.
Fearful dogs, in my opinion, are fearful dogs. My observations of my own fear-agressive dog is this.Some things may not bother them (noise, people,children, back firing cars) enough to react, but it is still to some degree be stressful.
Although Tiki was a bouvier and acted stoic, in true bouv fashion, she was fearful. My job, as human, was to never put her in a spot where she had to make a decision. Her job was to trust me to look after things for her. She came everywhere with me, I expected her to behave nicely. I watched her like a hawk for signs for stress and never put her in situations where she had to decide how to react. Her reactions came from a place that was scared, not confident. She was abused, lived in a puppy mill, used for breeding and left behind (freed) when the owners moved. It took a neighbor 2 weeks to gain her trust. She was simply the sweetest dog and the oldest soul I've ever known. BUT she couldn't be allowed to React.
After years of living with me and building confidence in me, she still would not comfortably get into bed with me. It was too high (dog language, not physical height). She would get up and wait for me to fall asleep, then get down onto the floor.
Have you given "Grounding" a good 8 week shot? It seems like you have a few things going on (and stacked against you).
1. Zeke is a Border Collie. These dogs, in my opinion, make it their life's work to find a job. 24/7. Gypsy is there conveniently those same hours
2. Fearful actions, and when that "scene" hasn't played out the same as always (posturing), he is now in a position to "react" in a new way which equal more stress.
3. More stress. He's gotten away with his "ground zero" behaviour and now needs to "decide" how to progress. Because his decision come from "fear" they will be poor ones.
Zeke needs to understand that you will look after all things dog. There should be a clear line drawn on this behaviour. The actual "dominance" with Gypsy isn't the problem, it's the symptom. You need to find the "first step". Maybe it's after you've brought in groceries and excitement is too much and that's how he burns it off. Maybe he's overtired, like a child. You've worked with him too hard/far.
It sounds to me like Gypsy is not the type of dog you could "let work this out". She's too laid back and respectful. Some dogs, yes, you could, Gypsy...nope. I would be afraid of what it's doing to Gypsy's trust in you.
I believe Zeke will continue (spiral, if you will) from here. His responsibilities are more than he can handle now (judging from his behaviour), which will cause more stress, and more poor decisions.I don't consider it a "fault" more of a "behaviour trait" that you learn to live with.
Again...First: I'd ground him. Second:Figure out what's starting the behaviour, avoid it, if possible, or prepare to distract/calm whatever he needs to avoid escalation.
PS... Great news on the antlers!