That original post was for Gimp 2.8 but 2.8 or 2.10 I can not reproduce the problem in normal use and I use the clone tool a lot.
Can you give more details, a screenshot showing tool options and layer modes often helps find a solution.
This is a standard setup (tool options detached so everything shows) using the clone tool in registered mode, cloning from layer-to-layer and when I difference the layers get the expected, they cancel each other out no difference between them https://i.imgur.com/rHqjMJy.mp4
As a start check tool mode / tool opacity / layer opacity / layer mode. Does it happen with all brush types ?
Can you give more details, a screenshot showing tool options and layer modes often helps find a solution.
This is a standard setup (tool options detached so everything shows) using the clone tool in registered mode, cloning from layer-to-layer and when I difference the layers get the expected, they cancel each other out no difference between them https://i.imgur.com/rHqjMJy.mp4
As a start check tool mode / tool opacity / layer opacity / layer mode. Does it happen with all brush types ?