There is a setting in the Workarounds section to add/subtract pixels when calculating how to place and size popups.
For example: if you have a rule that sets x=0 and width=100, and use this setting to add 10 to X and subtract 20 from the width, the result simulates a 10 pixel gap on the left and right sides.

Note that this only applies when the popup is opened and placed by the extension, **it's not possible to add a real invisible border** to a window from an extension. If you use for example Windows Snap afterwards then the popup will not have a gap between itself and the other window.

Edit: Sorry, I still don't understand what you are asking for, can you clarify? This is what I refer to as "invisible border": https://i.imgur.com/3fEz63K.png (It's only a problem in Windows 10 as far as I know)
(Edit 2): Maybe I understand... Do you mean the title bar that's supposed to be to the left of the minimize/maximize/close buttons but is gone in your image? That's not something I am explicitly able to hide, and I don't want to add features that relies on bugs in order to work.