
Ok, a couple of thoughts.
Firstly, you can't "emphasise her being top dog": we don't get to decide that, if indeed there's a hierarchy at all. Often there isn't, between dogs. So feeding order doesn't make much different unless a particular dog gets anxious about being fed first or last.
Running off is unlikely to be a way of "asserting herself" but it may well be a way to get your attention, depending on how you react: if you only spring to life when she runs off, to try and get her back, then absolutely! So you could try increasing rewards and attention when she's nearby. Reward her for not running off in the first place (i.e. hanging around with you). It sounds more like running off and doing her own thing is just more reinforcing to her than coming back to you though, rather than it being attention-seeking, but my advice would be the same thing. Reward more for hanging around with you, to make that more reinforcing, not only when she comes back from running off.
And to be honest, I would still query whether there's something underlying, because her behaviour is unusual for a GR. Only trotting stands out to me too. Even regular health check ups can easily miss stuff (I see it all the time through behaviour cases, because they aren't typically investigatory - it's listening to the heart, checking eyes/ears/teeth, and not much more), unless you specifically ask for joint manipulation and spinal check, or ask for other investigations such as bloods or looking into gut function. Gut discomfort affecting behaviour is a very common issue that gets missed very often, and in many cases, the only symptom is behavioural. I would wonder if she's always been in a degree of mild discomfort, potentially from birth.
Your younger dog could be a factor yes, but that wouldn't change my approach tbh - consider medical possibilities and reward for staying nearby.