10-09-2021, 06:37 PM
Really you answered the question yourself at the beginning. The origin of the pattern fill is zero, zero - ie. top left corner. That applies to layers as well as the canvas. If you can make your area a selected layer, even as a temporary layer it will fill from top left corner.
For that rectangle, a fuzzy select inside (with threshold up a bit to avoid anti-aliased pixels) and then a paste gives a floating selection layer. That still obeys the rules and fills. Then it is anchored to fill the rectangle.
Reads more complicated than it is: 30 second demo: https://i.imgur.com/1SuqZzE.mp4
For that rectangle, a fuzzy select inside (with threshold up a bit to avoid anti-aliased pixels) and then a paste gives a floating selection layer. That still obeys the rules and fills. Then it is anchored to fill the rectangle.
Reads more complicated than it is: 30 second demo: https://i.imgur.com/1SuqZzE.mp4