I think the issue is your block structure (HTML).
You could re-arrange your blocks or apply the clip path as a pseudo element to not clip/crop the child blocks.
Not sure if clip-path is even something you want to apply here, why not using a tilt separator instead?
You can try to apply a position of relative to the div where you added the separator.
The separator itself is an absolute positioned direct child, so it’s required to position its parent relatively.
I think the default block position inside the editor is relative, so there might be some discrepancies here and there.
As @Marius said, unfortunately Gutenberg adds a relative position to every block element.
So if you use an absolute position, be sure its parent is positioned relatively.