When you get to this point
Finally, when try to edit the transparent colour of the border, it changes the colour on the fill too; and vice versa!
are you now editing on the canvas with the Gradient tool?
What happens when you have a gradient on the fill and a separate gradient on the stroke of the same object, and depending on how you created the gradient, is that the gradient handles lie precisely right on top of each other. As far as I can tell, it's impossible to edit either one. In this case, the only way I've found to edit, is to drag the gradient handles apart. This does change how the gradient fills the fill or stroke, but after you make your changes, you can drag the handle back into place.
To drag the handles apart, hold Shift key while you grab the square handle and drag it away from the other. Those square handles are locked together, so you have to hold Shift to unlock them. And you have to drag it some distance, or it will snap back into its locked position.
However, the other day, I found out the old gradient editor isn't entirely gone! If you go into Inskcape Preferences > Tools > Gradient, put a check beside "Use legacy gradient editor", then go in the Fill and Stroke dialog and click the tiny pencil and paper icon on the bottom, left corner of the dialog. That opens the old editor

(An object with a gradient has to be selected, to see the icon.)
So, if you created the gradient by selecting the object, and clicking one of the gradient buttons in the Fill and Stroke dialog, it automatically creates the gradient centered in the object's fill and/or stroke. And that's how they become stuck on top of each other. But if you create the gradient by dragging the gradient tool over the object, you can see to it that the handles are already separated. Then you can drag them together later, if you need to. Just remember when you're dragging the gradient handles, when they get close to each other, they will automatically snap and be locked together -- no matter whether you have snapping enabled or not! And also remember that the Shift key is the key to unlocking them

If that doesn't answer your question, would you please explain in detaill exactly the steps you take -- which buttons you click or what tool you're using, what you do on the canvas, etc.