I admit, without a video, I’m having trouble understanding what you are seeing. As far as I can tell, we have a nearly identical display arrangement: my MacBookPro sitting on my desk with my larger external display sitting directly above it; the MBP Retina display being the primary display.
Window position is controlled my macOS, so I’m not sure what we could do even if we could reproduce it. That said, window size is something that is recorded in Rhino’s preferences file …and, even though I don’t know how macOS determines the complex arrangement of window layout within the various spaces on the various displays - I do imagine macOS needs to know what the size is. You might try backing up and then resetting your Rhino preferences to see if it changes things.
In my experience, Dock position is often critical to where windows get placed when the application launches. I don’t know if you’ve noticed this, but one downside of the arrangement you and I seem to share is that getting the actual Dock to appear on the larger, upper display is pretty awkward…for me it involves moving my mouse to the right or the left-hand side of the extents of the upper display, but only to the right or left of the display below. I don’t know if this is relevant to what you are seeing - but I do know that dock location seems to dictate where macOS decides to place the window on launch.